diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 3ea49a05..d9d42647 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -61,25 +61,7 @@ updates:
       - "automated"
       - "security"
 
-  - package-ecosystem: "cargo"
-    directory: "/tools/wizer_initializer"
-    schedule:
-      interval: "weekly"
-      day: "monday"
-      time: "06:00"
-    open-pull-requests-limit: 10
-    reviewers:
-      - "avrabe"
-    assignees:
-      - "avrabe"
-    commit-message:
-      prefix: "rust/wizer"
-      include: "scope"
-    labels:
-      - "dependencies"
-      - "rust"
-      - "automated"
-      - "performance"
+  # Note: /tools/wizer_initializer removed - wizer is now part of wasmtime v39.0.0+
 
   - package-ecosystem: "cargo"
     directory: "/tools-builder/toolchains"
diff --git a/CLAUDE.md b/CLAUDE.md
index 448ed034..ec20f69b 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -75,14 +75,13 @@ Before implementing any solution:
 
 5. **Medium files IMPROVED** - 5 → 3 calls (-2)
    - ✅ wkg_toolchain.bzl: cp → symlink
-   - ✅ wizer_toolchain.bzl: which → repository_ctx.which()
+   - ✅ wizer_toolchain.bzl: REMOVED (wizer now part of wasmtime v39.0.0+)
 
-**REMAINING COMPLEX OPERATIONS (31 calls):**
+**REMAINING COMPLEX OPERATIONS (29 calls):**
 
 - **wasm_toolchain.bzl (17)**: Remaining download and build operations (hybrid approach working)
 - **tool_cache.bzl (6)**: Tool validation and file existence checks
 - **tinygo_toolchain.bzl (3)**: Tool installation and validation
-- **wizer_toolchain.bzl (2)**: Script execution and version checking
 - **Others (3)**: Package management and validation
 
 **Shell Operation Categories MODERNIZED:**
@@ -155,94 +154,48 @@ These remaining shell scripts are **appropriate complexity** for their tasks:
 
 ## WIZER INTEGRATION STATUS
 
-### 🎯 Complete Solution Architecture Implemented
+### ✅ MIGRATION COMPLETE: Wasmtime v39.0.0+ Integration
 
-**Problem**: Wizer CLI expects WebAssembly modules but WASI-enabled Rust toolchain produces components
+**As of November 2025**, Wizer has been merged into Wasmtime and is available as the `wasmtime wizer` subcommand.
+This eliminates the need for a standalone wizer toolchain and simplifies dependency management.
 
-**Solution**: Library-based approach with component parsing
+### Architecture
 
-### ✅ COMPLETED COMPONENTS
+The wizer pre-initialization workflow now uses wasmtime's built-in wizer subcommand:
 
-1. **wizer_initializer Tool** (`//tools/wizer_initializer:wizer_initializer`)
-   - ✅ Bazel-native Rust binary with proper dependency management
-   - ✅ Component model detection (version 0x1000d vs 0x1)
-   - ✅ Architecture for component → module → wizer → component workflow
-   - ✅ Placeholder implementation demonstrating complete pipeline
-   - ✅ Full CLI interface with clap and anyhow
+1. **wasm_component_wizer Rule** (`//wasm:wasm_component_wizer.bzl`)
+   - Uses `wasmtime_toolchain_type` instead of standalone wizer
+   - Invokes `wasmtime wizer` subcommand
+   - Default init function: `wizer-initialize` (breaking change from `wizer.initialize`)
 
 2. **wasm_component_wizer_library Rule** (`//wasm:wasm_component_wizer_library.bzl`)
-   - ✅ Bazel rule using wizer_initializer for programmatic control
-   - ✅ Proper argument passing (--input, --output, --init-func, --allow-wasi, --verbose)
-   - ✅ Full integration with existing Bazel ecosystem
-   - ✅ Successfully tested with wizer_example
+   - Library-based pre-initialization support
+   - Uses wasmtime toolchain for wizer functionality
 
-3. **Working Integration Test** (`//examples/wizer_example:wizer_library_test`)
-   - ✅ Successfully processes WebAssembly components (2.2MB test file)
-   - ✅ Correct component model detection and verbose logging
-   - ✅ Demonstrates complete architecture end-to-end
+3. **Working Example** (`//examples/wizer_example`)
+   - Demonstrates pre-initialization with wasmtime wizer
+   - Uses `#[export_name = "wizer-initialize"]` (new naming convention)
 
-### 🔧 CURRENT IMPLEMENTATION STATUS
+### Breaking Changes (Issue #246)
 
-**Working Foundation:**
+- Init function name changed: `wizer.initialize` → `wizer-initialize`
+- Standalone wizer toolchain removed (use wasmtime toolchain)
+- `//tools/wizer_initializer` removed (no longer needed)
+- `checksums/tools/wizer.json` removed
 
-- ✅ Component/module format detection working perfectly
-- ✅ Bazel rule integration working with proper error handling
-- ✅ CLI argument processing and verbose logging working
-- ✅ File I/O and Bazel integration working flawlessly
-
-**Placeholder Components (for dependency resolution issues):**
-
-- ⏳ Component parsing (requires wasm-tools or wasmtime integration)
-- ⏳ Wizer library calls (requires wizer crate - complex dependencies)
-- ⏳ Component wrapping (requires wasm-tools component new functionality)
-
-### 🚀 ARCHITECTURE SUCCESS
-
-The implemented solution **perfectly demonstrates** the correct approach:
+### Migration Guide
 
+**Before (standalone wizer):**
 ```rust
-// Workflow: Component → Core Module → Wizer → Component
-let is_component = is_wasm_component(&input_bytes)?;  // ✅ Working
-let core_module = extract_core_module(&input_bytes)?;  // ⏳ Placeholder
-let initialized = wizer.run(&core_module)?;           // ⏳ Placeholder
-let final_component = wrap_as_component(&initialized)?; // ⏳ Placeholder
+#[export_name = "wizer.initialize"]
+pub extern "C" fn init() { ... }
 ```
 
-**Key Achievement**: The Bazel integration and component detection work perfectly. The remaining work is adding the
-specific crate dependencies for:
-
-1. `wasm-tools` for component parsing/wrapping
-2. `wizer` crate for actual pre-initialization
-3. `wasmtime` for runtime component support
-
-### 🔬 COMPLEX DEPENDENCY ANALYSIS
-
-**Issue**: Bazel crate_universe has build conflicts with Wizer/Wasmtime ecosystem:
-
-- Cranelift (used by Wasmtime) has complex ISLE build system requirements
-- Version conflicts between transitive dependencies
-- Build script compatibility issues in sandboxed Bazel environment
-
-**Alternative Approaches**:
-
-1. **Shell out to system wizer** (against Bazel principles)
-2. **Hermetic wasm-tools + wizer binaries** (current working approach with CLI)
-3. **Library integration** (implemented architecture, requires dependency resolution)
-
-### 📊 CURRENT STATE SUMMARY
-
-| Component              | Status         | Notes                                  |
-| ---------------------- | -------------- | -------------------------------------- |
-| Architecture Design    | ✅ Complete    | Library-based approach validated       |
-| Bazel Rule Integration | ✅ Complete    | wasm_component_wizer_library working   |
-| Component Detection    | ✅ Complete    | Perfect WebAssembly format detection   |
-| CLI Tool Framework     | ✅ Complete    | Full argument processing and logging   |
-| Test Integration       | ✅ Complete    | Working end-to-end in wizer_example    |
-| Wizer Library Calls    | ⏳ Placeholder | Requires complex dependency resolution |
-| Component Parsing      | ⏳ Placeholder | Requires wasm-tools or wasmtime crates |
-
-**Bottom Line**: The architecture is complete and proven. The remaining work is purely dependency management for the
-Wizer/Wasmtime ecosystem in Bazel.
+**After (wasmtime wizer):**
+```rust
+#[export_name = "wizer-initialize"]
+pub extern "C" fn init() { ... }
+```
 
 #### 📋 Implementation Guidelines
 
diff --git a/MODULE.bazel b/MODULE.bazel
index cf92f9bc..3cb6d06a 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -171,18 +171,8 @@ use_repo(tinygo, "tinygo_toolchain")
 
 register_toolchains("@tinygo_toolchain//:tinygo_toolchain_def")
 
-# Wizer WebAssembly pre-initialization toolchain
-wizer = use_extension("//wasm:extensions.bzl", "wizer")
-wizer.register(
-    name = "wizer",
-    strategy = "download",
-    version = "10.0.0",
-)
-use_repo(wizer, "wizer_toolchain")
-
-register_toolchains("@wizer_toolchain//:wizer_toolchain_def")
-
-# Wasmtime WebAssembly runtime
+# Wasmtime WebAssembly runtime (includes wizer as of v39.0.0)
+# Note: Standalone wizer toolchain removed - use `wasmtime wizer` subcommand instead
 wasmtime = use_extension("//wasm:extensions.bzl", "wasmtime")
 wasmtime.register(
     name = "wasmtime",
@@ -262,11 +252,6 @@ register_toolchains("//toolchains:wasm_tools_component_toolchain_local")
 
 # Rust crates for tools
 crate = use_extension("@rules_rust//crate_universe:extension.bzl", "crate")
-crate.from_cargo(
-    name = "wizer_crates",
-    cargo_lockfile = "//tools/wizer_initializer:Cargo.lock",
-    manifests = ["//tools/wizer_initializer:Cargo.toml"],
-)
 crate.from_cargo(
     name = "crates",
     cargo_lockfile = "//tools/checksum_updater:Cargo.lock",
@@ -325,7 +310,7 @@ crate.from_cargo(
 #   - wit_bindgen::rt module with correct allocator integration
 # This replaces the previously embedded runtime stubs
 
-use_repo(crate, "crates", "ssh_keygen_crates", "wasm_embed_aot_crates", "wasmsign2_crates", "wizer_crates")
+use_repo(crate, "crates", "ssh_keygen_crates", "wasm_embed_aot_crates", "wasmsign2_crates")
 
 # Modernized WASM tool repositories using git_repository + rules_rust
 wasm_tool_repos = use_extension("//toolchains:extensions.bzl", "wasm_tool_repositories")
@@ -335,6 +320,5 @@ use_repo(
     "wasm_tools_src",
     "wasmsign2_src",
     "wit_bindgen_src",
-    "wizer_src",
     "wrpc_src",
 )
diff --git a/checksums/registry.bzl b/checksums/registry.bzl
index 0b7c51f5..766a5489 100644
--- a/checksums/registry.bzl
+++ b/checksums/registry.bzl
@@ -781,73 +781,7 @@ def _get_fallback_checksums(tool_name):
                 },
             },
         },
-        "wizer": {
-            "tool_name": "wizer",
-            "github_repo": "bytecodealliance/wizer",
-            "latest_version": "10.0.0",
-            "versions": {
-                "10.0.0": {
-                    "release_date": "2025-08-27",
-                    "platforms": {
-                        "darwin_amd64": {
-                            "sha256": "d6b2073efb38624399c1c6fc0d8c1e19ba24d7ab934f51c346b7d97d4bd8115c",
-                            "url_suffix": "x86_64-macos.tar.xz",
-                            "strip_prefix": "wizer-v10.0.0-x86_64-macos",
-                        },
-                        "darwin_arm64": {
-                            "sha256": "5e3977e25defc869141dd8df3d25dde1dabe37ea377b7c01fa24693fe5bc7b3f",
-                            "url_suffix": "aarch64-macos.tar.xz",
-                            "strip_prefix": "wizer-v10.0.0-aarch64-macos",
-                        },
-                        "linux_amd64": {
-                            "sha256": "1e9dfaa2f6c436ca7acfdbb82c166f5b8a0062068f12916a554e82c97ca8d371",
-                            "url_suffix": "x86_64-linux.tar.xz",
-                            "strip_prefix": "wizer-v10.0.0-x86_64-linux",
-                        },
-                        "linux_arm64": {
-                            "sha256": "8ec7e50622aa7af37b5152f19d7a371f185c7af138033759caa3fdd3e17e2830",
-                            "url_suffix": "aarch64-linux.tar.xz",
-                            "strip_prefix": "wizer-v10.0.0-aarch64-linux",
-                        },
-                        "windows_amd64": {
-                            "sha256": "29a3aebb70927e9af7c505d3f3d14c5f8577eb307e8bd45151c184885a580d2f",
-                            "url_suffix": "x86_64-windows.zip",
-                            "strip_prefix": "wizer-v10.0.0-x86_64-windows",
-                        },
-                    },
-                },
-                "9.0.0": {
-                    "release_date": "2024-06-03",
-                    "platforms": {
-                        "darwin_amd64": {
-                            "sha256": "5d5e457abf3fd6e307dee9fe9f7423185a88d90f0c96677b9a5418c448ced52e",
-                            "url_suffix": "x86_64-macos.tar.xz",
-                            "strip_prefix": "wizer-v9.0.0-x86_64-macos",
-                        },
-                        "darwin_arm64": {
-                            "sha256": "3372ee8215abc39b15a51b4aed27f8ae5a42e84261a29e7491ec82bf806bc491",
-                            "url_suffix": "aarch64-macos.tar.xz",
-                            "strip_prefix": "wizer-v9.0.0-aarch64-macos",
-                        },
-                        "linux_amd64": {
-                            "sha256": "d1d85703bc40f18535e673992bef723dc3f84e074bcd1e05b57f24d5adb4f058",
-                            "url_suffix": "x86_64-linux.tar.xz",
-                            "strip_prefix": "wizer-v9.0.0-x86_64-linux",
-                        },
-                        "linux_arm64": {
-                            "sha256": "f560a675d686d42c18de8bd4014a34a0e8b95dafbd696bf8d54817311ae87a4d",
-                            "url_suffix": "aarch64-linux.tar.xz",
-                            "strip_prefix": "wizer-v9.0.0-aarch64-linux",
-                        },
-                        "windows_amd64": {
-                            "sha256": "d9cc5ed028ca873f40adcac513812970d34dd08cec4397ffc5a47d4acee8e782",
-                            "url_suffix": "x86_64-windows.zip",
-                            "strip_prefix": "wizer-v9.0.0-x86_64-windows",
-                        },
-                    },
-                },
-            },
-        },
+        # Note: wizer removed - now part of wasmtime v39.0.0+, use `wasmtime wizer` subcommand
         "jco": {
             "tool_name": "jco",
             "github_repo": "bytecodealliance/jco",
@@ -1013,6 +947,7 @@ def list_available_tools():
     """
 
     # Return tools that have fallback data available
+    # Note: wizer removed - now part of wasmtime v39.0.0+, use `wasmtime wizer` subcommand
     return [
         "wasm-tools",
         "wit-bindgen",
@@ -1021,7 +956,6 @@ def list_available_tools():
         "wasmtime",
         "wasi-sdk",
         "wasmsign2",
-        "wizer",
         "nodejs",
         "jco",
         "file-ops-component",
diff --git a/checksums/registry_test.bzl b/checksums/registry_test.bzl
index be12a1d3..c34a2029 100644
--- a/checksums/registry_test.bzl
+++ b/checksums/registry_test.bzl
@@ -20,9 +20,9 @@ def _test_get_tool_checksum(ctx):
     checksum = get_tool_checksum("wasm-tools", "1.235.0", "darwin_amd64")
     asserts.equals(env, "154e9ea5f5477aa57466cfb10e44bc62ef537e32bf13d1c35ceb4fedd9921510", checksum)
 
-    # Test wizer checksum (our new addition)
-    wizer_checksum = get_tool_checksum("wizer", "9.0.0", "linux_amd64")
-    asserts.equals(env, "d1d85703bc40f18535e673992bef723dc3f84e074bcd1e05b57f24d5adb4f058", wizer_checksum)
+    # Test wasmtime checksum (wizer functionality now included in wasmtime v39.0.0+)
+    wasmtime_checksum = get_tool_checksum("wasmtime", "39.0.1", "linux_amd64")
+    asserts.equals(env, "b90a36125387b75db59a67a1c402f2ed9d120fa43670d218a559571e2423d925", wasmtime_checksum)
 
     # Test invalid tool
     invalid_checksum = get_tool_checksum("nonexistent-tool", "1.0.0", "linux_amd64")
@@ -48,11 +48,11 @@ def _test_get_tool_info(ctx):
     asserts.equals(env, "154e9ea5f5477aa57466cfb10e44bc62ef537e32bf13d1c35ceb4fedd9921510", info["sha256"])
     asserts.equals(env, "x86_64-macos.tar.gz", info["url_suffix"])
 
-    # Test wizer info
-    wizer_info = get_tool_info("wizer", "9.0.0", "windows_amd64")
-    asserts.true(env, wizer_info != None)
-    asserts.equals(env, "d9cc5ed028ca873f40adcac513812970d34dd08cec4397ffc5a47d4acee8e782", wizer_info["sha256"])
-    asserts.equals(env, "x86_64-windows.zip", wizer_info["url_suffix"])
+    # Test wasmtime info (wizer functionality now included in wasmtime v39.0.0+)
+    wasmtime_info = get_tool_info("wasmtime", "39.0.1", "windows_amd64")
+    asserts.true(env, wasmtime_info != None)
+    asserts.equals(env, "bccf64b4227d178c0d13f2856be68876eae3f2f657f3a85d46f076a5e1976198", wasmtime_info["sha256"])
+    asserts.equals(env, "x86_64-windows.zip", wasmtime_info["url_suffix"])
 
     return unittest.end(env)
 
@@ -79,12 +79,12 @@ def _test_list_supported_platforms(ctx):
     asserts.true(env, "linux_amd64" in platforms)
     asserts.true(env, "windows_amd64" in platforms)
 
-    # Test wizer platforms
-    wizer_platforms = list_supported_platforms("wizer", "9.0.0")
-    asserts.true(env, "darwin_amd64" in wizer_platforms)
-    asserts.true(env, "linux_amd64" in wizer_platforms)
-    asserts.true(env, "windows_amd64" in wizer_platforms)
-    asserts.equals(env, 5, len(wizer_platforms))  # Should have 5 platforms
+    # Test wasmtime platforms (wizer functionality now included in wasmtime v39.0.0+)
+    wasmtime_platforms = list_supported_platforms("wasmtime", "39.0.1")
+    asserts.true(env, "darwin_amd64" in wasmtime_platforms)
+    asserts.true(env, "linux_amd64" in wasmtime_platforms)
+    asserts.true(env, "windows_amd64" in wasmtime_platforms)
+    asserts.equals(env, 5, len(wasmtime_platforms))  # Should have 5 platforms
 
     return unittest.end(env)
 
@@ -95,7 +95,7 @@ def _test_get_github_repo(ctx):
     # Test known repos
     asserts.equals(env, "bytecodealliance/wasm-tools", get_github_repo("wasm-tools"))
     asserts.equals(env, "bytecodealliance/wit-bindgen", get_github_repo("wit-bindgen"))
-    asserts.equals(env, "bytecodealliance/wizer", get_github_repo("wizer"))
+    asserts.equals(env, "bytecodealliance/wasmtime", get_github_repo("wasmtime"))
 
     # Test invalid tool
     asserts.equals(env, None, get_github_repo("nonexistent-tool"))
@@ -108,7 +108,7 @@ def _test_validate_tool_exists(ctx):
 
     # Test valid combinations
     asserts.true(env, validate_tool_exists("wasm-tools", "1.235.0", "darwin_amd64"))
-    asserts.true(env, validate_tool_exists("wizer", "9.0.0", "linux_amd64"))
+    asserts.true(env, validate_tool_exists("wasmtime", "39.0.1", "linux_amd64"))
 
     # Test invalid combinations
     asserts.false(env, validate_tool_exists("nonexistent-tool", "1.0.0", "linux_amd64"))
@@ -124,7 +124,7 @@ def _test_list_available_tools(ctx):
     tools = list_available_tools()
     asserts.true(env, "wasm-tools" in tools)
     asserts.true(env, "wit-bindgen" in tools)
-    asserts.true(env, "wizer" in tools)
+    asserts.true(env, "wasmtime" in tools)  # wizer functionality now in wasmtime
     asserts.true(env, "wac" in tools)
     asserts.true(env, "wkg" in tools)
 
diff --git a/checksums/toolchain_bundles.json b/checksums/toolchain_bundles.json
index 9b95e670..8bd7badb 100644
--- a/checksums/toolchain_bundles.json
+++ b/checksums/toolchain_bundles.json
@@ -12,7 +12,6 @@
         "wac": "0.8.1",
         "wkg": "0.13.0",
         "wasmtime": "39.0.1",
-        "wizer": "10.0.0",
         "wasi-sdk": "29",
         "tinygo": "0.38.0",
         "jco": "1.4.0",
@@ -30,7 +29,7 @@
         "linux_arm64",
         "windows_amd64"
       ],
-      "notes": "Initial stable bundle with WASI Preview 2 support"
+      "notes": "Initial stable bundle with WASI Preview 2 support. Wizer functionality now included in wasmtime v39.0.0+"
     },
     "minimal": {
       "description": "Minimal bundle for basic WASM component builds",
@@ -100,13 +99,6 @@
           {"wasmtime": "39.0.1", "wasm-tools": "1.243.0"},
           {"wasmtime": "29.0.0", "wasm-tools": "1.240.0"}
         ]
-      },
-      {
-        "tools": ["wizer", "wasmtime"],
-        "rule": "wizer and wasmtime should use compatible cranelift versions",
-        "validated_pairs": [
-          {"wizer": "10.0.0", "wasmtime": "39.0.1"}
-        ]
       }
     ]
   }
diff --git a/checksums/tools/wizer.json b/checksums/tools/wizer.json
deleted file mode 100644
index b26161a3..00000000
--- a/checksums/tools/wizer.json
+++ /dev/null
@@ -1,75 +0,0 @@
-{
-  "tool_name": "wizer",
-  "github_repo": "bytecodealliance/wizer",
-  "latest_version": "10.0.0",
-  "last_checked": "2025-12-04T00:00:00.000000Z",
-  "supported_platforms": [
-    "darwin_amd64",
-    "darwin_arm64",
-    "linux_amd64",
-    "linux_arm64",
-    "windows_amd64"
-  ],
-  "versions": {
-    "10.0.0": {
-      "release_date": "2025-08-27",
-      "platforms": {
-        "darwin_amd64": {
-          "sha256": "d6b2073efb38624399c1c6fc0d8c1e19ba24d7ab934f51c346b7d97d4bd8115c",
-          "url_suffix": "x86_64-macos.tar.xz",
-          "strip_prefix": "wizer-v10.0.0-x86_64-macos"
-        },
-        "darwin_arm64": {
-          "sha256": "5e3977e25defc869141dd8df3d25dde1dabe37ea377b7c01fa24693fe5bc7b3f",
-          "url_suffix": "aarch64-macos.tar.xz",
-          "strip_prefix": "wizer-v10.0.0-aarch64-macos"
-        },
-        "linux_amd64": {
-          "sha256": "1e9dfaa2f6c436ca7acfdbb82c166f5b8a0062068f12916a554e82c97ca8d371",
-          "url_suffix": "x86_64-linux.tar.xz",
-          "strip_prefix": "wizer-v10.0.0-x86_64-linux"
-        },
-        "linux_arm64": {
-          "sha256": "8ec7e50622aa7af37b5152f19d7a371f185c7af138033759caa3fdd3e17e2830",
-          "url_suffix": "aarch64-linux.tar.xz",
-          "strip_prefix": "wizer-v10.0.0-aarch64-linux"
-        },
-        "windows_amd64": {
-          "sha256": "29a3aebb70927e9af7c505d3f3d14c5f8577eb307e8bd45151c184885a580d2f",
-          "url_suffix": "x86_64-windows.zip",
-          "strip_prefix": "wizer-v10.0.0-x86_64-windows"
-        }
-      }
-    },
-    "9.0.0": {
-      "release_date": "2024-06-03",
-      "platforms": {
-        "darwin_amd64": {
-          "sha256": "5d5e457abf3fd6e307dee9fe9f7423185a88d90f0c96677b9a5418c448ced52e",
-          "url_suffix": "x86_64-macos.tar.xz",
-          "strip_prefix": "wizer-v9.0.0-x86_64-macos"
-        },
-        "darwin_arm64": {
-          "sha256": "3372ee8215abc39b15a51b4aed27f8ae5a42e84261a29e7491ec82bf806bc491",
-          "url_suffix": "aarch64-macos.tar.xz",
-          "strip_prefix": "wizer-v9.0.0-aarch64-macos"
-        },
-        "linux_amd64": {
-          "sha256": "d1d85703bc40f18535e673992bef723dc3f84e074bcd1e05b57f24d5adb4f058",
-          "url_suffix": "x86_64-linux.tar.xz",
-          "strip_prefix": "wizer-v9.0.0-x86_64-linux"
-        },
-        "linux_arm64": {
-          "sha256": "f560a675d686d42c18de8bd4014a34a0e8b95dafbd696bf8d54817311ae87a4d",
-          "url_suffix": "aarch64-linux.tar.xz",
-          "strip_prefix": "wizer-v9.0.0-aarch64-linux"
-        },
-        "windows_amd64": {
-          "sha256": "d9cc5ed028ca873f40adcac513812970d34dd08cec4397ffc5a47d4acee8e782",
-          "url_suffix": "x86_64-windows.zip",
-          "strip_prefix": "wizer-v9.0.0-x86_64-windows"
-        }
-      }
-    }
-  }
-}
diff --git a/docs-site/src/content/docs/guides/toolchain-configuration.md b/docs-site/src/content/docs/guides/toolchain-configuration.md
index d976a6df..8cfc48a0 100644
--- a/docs-site/src/content/docs/guides/toolchain-configuration.md
+++ b/docs-site/src/content/docs/guides/toolchain-configuration.md
@@ -64,9 +64,11 @@ wasm_toolchain.register(
 | wkg_toolchain   | ✅       | ✅    | ❌     | ❌  | ❌    |
 | jco_toolchain   | ✅       | ❌    | ❌     | ✅  | ❌    |
 | cpp_component   | ✅       | ✅    | ❌     | ❌  | ❌    |
-| wizer_toolchain | ✅       | ✅    | ❌     | ❌  | ✅    |
 | wasmtime        | ✅       | ❌    | ❌     | ❌  | ❌    |
 
+> **Note:** Wizer functionality is now included in wasmtime v39.0.0+ via the `wasmtime wizer` subcommand.
+> No separate wizer_toolchain is required.
+
 ### When to Use Each Strategy
 
 #### `"download"` (Default) - Hermetic & Fast
@@ -164,13 +166,14 @@ jco.register(
 
 #### `"cargo"` - Rust Ecosystem
 
-**Best for:** Rust-heavy projects, when you need Wizer
+**Best for:** Rust-heavy projects building from source
 
 ```python title="MODULE.bazel"
-wizer = use_extension("@rules_wasm_component//wasm:extensions.bzl", "wizer")
-wizer.register(
+# Example: building wasm-tools from source via cargo
+wasm_toolchain = use_extension("@rules_wasm_component//wasm:extensions.bzl", "wasm_toolchain")
+wasm_toolchain.register(
     strategy = "cargo",    # Uses cargo install
-    version = "9.0.0",
+    version = "1.243.0",
 )
 ```
 
@@ -184,7 +187,9 @@ wizer.register(
 
 - **Rust required** - System dependency
 - **Compilation time** - Builds from source
-- **Wizer only** - Limited to Wizer toolchain
+- **Limited toolchains** - Not all toolchains support cargo strategy
+
+> **Note:** The standalone wizer toolchain has been removed. Wizer is now part of wasmtime v39.0.0+ and available via the `wasmtime wizer` subcommand.
 
 ## Performance Comparison
 
@@ -423,17 +428,20 @@ bazel build //... --jobs=auto --local_ram_resources=8192
 
 #### Wizer Pre-initialization
 
-For faster component startup:
+For faster component startup, use wasmtime's built-in wizer functionality (v39.0.0+):
 
 ```python title="MODULE.bazel - Performance"
-# Enable Wizer for startup optimization
-wizer = use_extension("@rules_wasm_component//wasm:extensions.bzl", "wizer")
-wizer.register(
-    strategy = "download",  # Fast, reliable
-    version = "9.0.0",
+# Wizer is included in wasmtime v39.0.0+
+# No separate wizer toolchain required - uses `wasmtime wizer` subcommand
+wasmtime = use_extension("@rules_wasm_component//wasm:extensions.bzl", "wasmtime")
+wasmtime.register(
+    strategy = "download",
+    version = "39.0.1",  # Includes wizer functionality
 )
 ```
 
+> **Note:** The init function name has changed from `wizer.initialize` to `wizer-initialize` in wasmtime's wizer.
+
 ## Troubleshooting
 
 ### Common Issues
diff --git a/docs/toolchain_configuration.md b/docs/toolchain_configuration.md
index 6cf53267..ec21f7d3 100644
--- a/docs/toolchain_configuration.md
+++ b/docs/toolchain_configuration.md
@@ -133,30 +133,22 @@ register_toolchains("@wasmtime_toolchain//:wasmtime_toolchain")
 - Testing infrastructure (`wasm_test`, `wasm_run`)
 - WASI Preview 2 support
 
-### Wizer Toolchain
+### Wizer (Pre-initialization)
 
-Default configuration (recommended):
-```starlark
-# MODULE.bazel - Included by default
-bazel_dep(name = "rules_wasm_component", version = "1.0.0")
-```
+> **Note:** As of wasmtime v39.0.0 (November 2025), Wizer has been integrated into wasmtime
+> and is available as the `wasmtime wizer` subcommand. No separate wizer toolchain is required.
 
-Custom version:
+Wizer pre-initialization is automatically available through the wasmtime toolchain:
 ```starlark
-wizer = use_extension("//wasm:extensions.bzl", "wizer")
-wizer.register(
-    name = "wizer",
-    strategy = "download",
-    version = "9.0.0",  # Or any other version
-)
-use_repo(wizer, "wizer_toolchain")
-register_toolchains("@wizer_toolchain//:wizer_toolchain_def")
+# MODULE.bazel - wasmtime toolchain includes wizer functionality
+bazel_dep(name = "rules_wasm_component", version = "1.0.0")
 ```
 
 **Features:**
 - Pre-initialization for 1.35-6x startup improvement
 - Component model support
 - WASI imports during initialization
+- Uses `wasmtime wizer` subcommand (not standalone wizer binary)
 
 ### wkg Toolchain
 
diff --git a/examples/wizer_example/BUILD.bazel b/examples/wizer_example/BUILD.bazel
index d5de65a8..5ec8b121 100644
--- a/examples/wizer_example/BUILD.bazel
+++ b/examples/wizer_example/BUILD.bazel
@@ -42,19 +42,20 @@ rust_wasm_component_bindgen(
     wit = ":expensive_init_interfaces",
 )
 
-# Apply Wizer to the WASM module
+# Apply Wizer to the WASM module using wasmtime wizer
+# Note: As of wasmtime v39.0.0, wizer is integrated into wasmtime
 wasm_component_wizer(
     name = "wizer_optimized_module",
     component = ":component_to_module",
-    init_function_name = "wizer.initialize",
+    init_function_name = "wizer-initialize",  # New default in wasmtime v39.0.0
 )
 
-# Test the new Wizer library-based approach
+# Test the wizer library-based approach (now uses wasmtime wizer)
 wasm_component_wizer_library(
     name = "wizer_library_test",
     allow_wasi = True,
     component = ":expensive_init_simple_module",
-    init_function_name = "wizer.initialize",
+    init_function_name = "wizer-initialize",  # New default in wasmtime v39.0.0
     verbose = True,
 )
 
diff --git a/examples/wizer_example/README.md b/examples/wizer_example/README.md
index 05b789cd..b06b1135 100644
--- a/examples/wizer_example/README.md
+++ b/examples/wizer_example/README.md
@@ -2,6 +2,8 @@
 
 This example demonstrates how to use Wizer for WebAssembly component pre-initialization to achieve dramatically improved startup performance.
 
+> **Note**: As of Wasmtime v39.0.0 (November 2025), the standalone Wizer tool has been merged upstream into Wasmtime. This example now uses the `wasmtime wizer` subcommand for pre-initialization.
+
 ## What is Wizer?
 
 Wizer is a WebAssembly pre-initialization tool that:
diff --git a/examples/wizer_example/src/lib.rs b/examples/wizer_example/src/lib.rs
index 1800805a..7407427a 100644
--- a/examples/wizer_example/src/lib.rs
+++ b/examples/wizer_example/src/lib.rs
@@ -23,7 +23,9 @@ impl Guest for Component {
 }
 
 // Wizer initialization function - runs at build time
-#[export_name = "wizer.initialize"]
+// Note: As of wasmtime v39.0.0, the default function name changed from
+// "wizer.initialize" to "wizer-initialize" for better component compatibility
+#[export_name = "wizer-initialize"]
 pub extern "C" fn wizer_initialize() {
     // Expensive computation that would normally happen at runtime
     let mut data = HashMap::new();
diff --git a/examples/wizer_example/src/lib_simple.rs b/examples/wizer_example/src/lib_simple.rs
index a5b2ad77..95431c76 100644
--- a/examples/wizer_example/src/lib_simple.rs
+++ b/examples/wizer_example/src/lib_simple.rs
@@ -17,7 +17,9 @@ pub extern "C" fn compute(input: i32) -> i32 {
 }
 
 // Wizer initialization function - runs at build time
-#[export_name = "wizer.initialize"]
+// Note: As of wasmtime v39.0.0, the default function name changed from
+// "wizer.initialize" to "wizer-initialize" for better component compatibility
+#[export_name = "wizer-initialize"]
 pub extern "C" fn wizer_initialize() {
     // Expensive computation that would normally happen at runtime
     let mut data = HashMap::new();
diff --git a/toolchains/BUILD.bazel b/toolchains/BUILD.bazel
index 40002648..525e8199 100644
--- a/toolchains/BUILD.bazel
+++ b/toolchains/BUILD.bazel
@@ -47,13 +47,8 @@ toolchain_type(
     visibility = ["//visibility:public"],
 )
 
-# Toolchain type for Wizer WebAssembly pre-initialization
-toolchain_type(
-    name = "wizer_toolchain_type",
-    visibility = ["//visibility:public"],
-)
-
 # Toolchain type for Wasmtime WebAssembly runtime
+# Note: Wizer functionality is now part of wasmtime (v39.0.0+), use wasmtime_toolchain_type
 toolchain_type(
     name = "wasmtime_toolchain_type",
     visibility = ["//visibility:public"],
@@ -135,18 +130,6 @@ bzl_library(
     ],
 )
 
-# Bzl library for Wizer WebAssembly pre-initialization toolchain implementation
-bzl_library(
-    name = "wizer_toolchain",
-    srcs = ["wizer_toolchain.bzl"],
-    visibility = ["//visibility:public"],
-    deps = [
-        ":diagnostics",
-        ":tool_cache",
-        "//checksums:registry",
-    ],
-)
-
 # Enhanced toolchain management libraries
 
 bzl_library(
diff --git a/toolchains/BUILD.wizer b/toolchains/BUILD.wizer
deleted file mode 100644
index b85f0fa2..00000000
--- a/toolchains/BUILD.wizer
+++ /dev/null
@@ -1,21 +0,0 @@
-"""BUILD file for wizer (WebAssembly pre-initialization tool) built from source"""
-
-load("@rules_rust//rust:defs.bzl", "rust_binary")
-
-rust_binary(
-    name = "wizer",
-    srcs = glob(["src/**/*.rs"]),
-    edition = "2021",
-    visibility = ["//visibility:public"],
-    deps = [
-        # Note: Dependencies will be resolved by rules_rust from Cargo.toml
-        # This follows the same pattern as other modernized tools
-    ],
-)
-
-# Alias for Bazel integration
-alias(
-    name = "wizer_bazel",
-    actual = ":wizer",
-    visibility = ["//visibility:public"],
-)
diff --git a/toolchains/tool_versions.bzl b/toolchains/tool_versions.bzl
index 3c952722..6c08b972 100644
--- a/toolchains/tool_versions.bzl
+++ b/toolchains/tool_versions.bzl
@@ -33,8 +33,7 @@ TOOL_VERSIONS = {
     "wac": "0.8.1",           # WebAssembly Composition tool
     "wkg": "0.13.0",          # WebAssembly package manager
 
-    # Optimization and initialization
-    "wizer": "10.0.0",        # WebAssembly pre-initialization tool
+    # Note: wizer removed - now part of wasmtime v39.0.0+, use `wasmtime wizer` subcommand
 
     # Signatures and security
     "wasmsign2": "0.2.6",     # WebAssembly signing tool
diff --git a/toolchains/wasm_tools_repositories.bzl b/toolchains/wasm_tools_repositories.bzl
index b017644f..8eb92967 100644
--- a/toolchains/wasm_tools_repositories.bzl
+++ b/toolchains/wasm_tools_repositories.bzl
@@ -63,13 +63,7 @@ def register_wasm_tool_repositories(bundle = None):
         build_file = "//toolchains:BUILD.wrpc",
     )
 
-    # wizer: WebAssembly pre-initialization tool
-    git_repository(
-        name = "wizer_src",
-        remote = "https://github.com/bytecodealliance/wizer.git",
-        tag = "v9.0.0",
-        build_file = "//toolchains:BUILD.wizer",
-    )
+    # Note: wizer removed - now part of wasmtime v39.0.0+, use `wasmtime wizer` subcommand
 
     # wasmsign2: WebAssembly component signing tool
     git_repository(
diff --git a/toolchains/wasmtime_toolchain.bzl b/toolchains/wasmtime_toolchain.bzl
index 24878805..e8d33bb0 100644
--- a/toolchains/wasmtime_toolchain.bzl
+++ b/toolchains/wasmtime_toolchain.bzl
@@ -172,7 +172,7 @@ wasmtime_repository = repository_rule(
         ),
         "version": attr.string(
             doc = "Wasmtime version to install. Ignored if bundle is specified.",
-            default = "35.0.0",  # Latest version from our registry
+            default = "39.0.1",  # Latest version with integrated wizer support
         ),
     },
     doc = "Repository rule for setting up Wasmtime WebAssembly runtime",
diff --git a/toolchains/wizer_toolchain.bzl b/toolchains/wizer_toolchain.bzl
deleted file mode 100644
index 6d1768e9..00000000
--- a/toolchains/wizer_toolchain.bzl
+++ /dev/null
@@ -1,318 +0,0 @@
-"""Wizer WebAssembly pre-initialization toolchain definitions"""
-
-load("//checksums:registry.bzl", "get_tool_info")
-load("//toolchains:bundle.bzl", "get_version_for_tool", "log_bundle_usage")
-
-WIZER_VERSIONS = {
-    "10.0.0": {
-        "release_date": "2025-08-27",
-        "cargo_install": True,  # Primary installation method
-        "git_commit": "main",
-    },
-    "9.0.0": {
-        "release_date": "2024-06-03",
-        "cargo_install": True,  # Primary installation method
-        "git_commit": "090082b",
-    },
-    "8.0.0": {
-        "release_date": "2024-02-28",
-        "cargo_install": True,
-        "git_commit": "unknown",
-    },
-}
-
-def _wizer_toolchain_impl(ctx):
-    """Implementation of wizer_toolchain rule"""
-
-    toolchain_info = platform_common.ToolchainInfo(
-        wizer = ctx.file.wizer,
-    )
-
-    return [toolchain_info]
-
-wizer_toolchain = rule(
-    implementation = _wizer_toolchain_impl,
-    attrs = {
-        "wizer": attr.label(
-            allow_single_file = True,
-            executable = True,
-            cfg = "exec",
-            doc = "Wizer pre-initialization tool executable",
-        ),
-    },
-)
-
-def _detect_host_platform(repository_ctx):
-    """Detect the host platform for tool installation"""
-    os_name = repository_ctx.os.name.lower()
-    arch = repository_ctx.os.arch.lower()
-
-    # Use Bazel's native architecture detection
-    if "mac" in os_name or "darwin" in os_name:
-        if arch == "aarch64" or "arm64" in arch:
-            return "darwin_arm64"
-        return "darwin_amd64"
-    elif "linux" in os_name:
-        if arch == "aarch64" or "arm64" in arch:
-            return "linux_arm64"
-        return "linux_amd64"
-    elif "windows" in os_name:
-        return "windows_amd64"
-    else:
-        fail("Unsupported operating system: {}".format(os_name))
-
-def _get_wizer_download_info(platform, version):
-    """Get download information for wizer prebuilt binaries from central registry"""
-
-    # Get tool info from central registry
-    tool_info = get_tool_info("wizer", version, platform)
-    if not tool_info:
-        fail("Unsupported platform {} for wizer version {}. Supported platforms can be found in //checksums/tools/wizer.json".format(platform, version))
-
-    # Build download URL
-    asset_name = "wizer-v{}-{}".format(version, tool_info["url_suffix"])
-    url = "https://github.com/bytecodealliance/wizer/releases/download/v{}/{}".format(version, asset_name)
-
-    # Determine archive type from suffix
-    archive_type = "zip" if tool_info["url_suffix"].endswith(".zip") else "tar.xz"
-
-    return {
-        "url": url,
-        "sha256": tool_info["sha256"],
-        "type": archive_type,
-        "strip_prefix": tool_info["strip_prefix"],
-    }
-
-def _wizer_toolchain_repository_impl(ctx):
-    """Implementation of wizer_toolchain_repository repository rule"""
-
-    strategy = ctx.attr.strategy
-    platform = _detect_host_platform(ctx)
-    bundle_name = ctx.attr.bundle
-
-    # Resolve version from bundle if specified, otherwise use explicit version
-    if bundle_name:
-        version = get_version_for_tool(
-            ctx,
-            "wizer",
-            bundle_name = bundle_name,
-            fallback_version = ctx.attr.version,
-        )
-        log_bundle_usage(ctx, "wizer", version, bundle_name)
-    else:
-        version = ctx.attr.version
-
-    if version not in WIZER_VERSIONS:
-        fail("Unsupported Wizer version: {}. Supported versions: {}".format(
-            version,
-            list(WIZER_VERSIONS.keys()),
-        ))
-
-    version_info = WIZER_VERSIONS[version]
-
-    if strategy == "build":
-        # Use the git repository + genrule approach for hermetic builds
-        print("Using hermetic build strategy with git_repository + genrule approach")
-
-        # Create a placeholder since the actual binary will be built by git repository
-        ctx.file("wizer", """#!/bin/bash
-# This is a placeholder - actual wizer is built by git_repository + genrule
-echo "Error: wizer should be accessed through Bazel targets, not as standalone binary"
-echo "Use the proper toolchain integration instead"
-exit 1
-""", executable = True)
-        wizer_path = "wizer"
-
-    elif strategy == "cargo":
-        # Create a script that installs Wizer via Cargo
-        ctx.file("install_wizer.sh", """#!/bin/bash
-set -euo pipefail
-
-WIZER_VERSION="{version}"
-INSTALL_DIR="$PWD/bin"
-
-# Ensure install directory exists
-mkdir -p "$INSTALL_DIR"
-
-# Check if cargo is available
-if ! command -v cargo &> /dev/null; then
-    echo "Error: cargo is required to install Wizer but is not available"
-    echo "Please install Rust and Cargo, or use strategy='system'"
-    exit 1
-fi
-
-# Install Wizer using cargo
-echo "Installing Wizer v$WIZER_VERSION via cargo..."
-cargo install wizer --version "=$WIZER_VERSION" --root . --all-features
-
-# Verify installation
-if [[ -f "$INSTALL_DIR/wizer" ]]; then
-    echo "Successfully installed Wizer v$WIZER_VERSION"
-    "$INSTALL_DIR/wizer" --version
-else
-    echo "Error: Wizer installation failed"
-    exit 1
-fi
-""".format(version = version), executable = True)
-
-        # Execute installation script
-        result = ctx.execute(["./install_wizer.sh"])
-        if result.return_code != 0:
-            # Check if the error is due to missing cargo (hermetic requirement)
-            if "cargo is required" in result.stderr or "cargo" in result.stderr:
-                print("Warning: Wizer installation skipped - cargo not available in hermetic environment")
-                print("This is expected in BCR testing environments")
-                print("Wizer functionality will be limited but basic WebAssembly builds will work")
-
-                # Create a placeholder wizer binary that explains the situation
-                ctx.file("bin/wizer", """#!/bin/bash
-echo "Wizer not available - cargo not accessible in hermetic environment"
-echo "This is expected in BCR testing environments"
-echo "WebAssembly pre-initialization functionality not available"
-echo "Use system strategy or ensure hermetic Rust toolchain is available"
-exit 1
-""", executable = True)
-                wizer_path = "bin/wizer"
-            else:
-                fail("Failed to install Wizer via cargo: {}".format(result.stderr))
-
-        wizer_path = "bin/wizer"
-
-    elif strategy == "source":
-        # Use git_repository approach (modernized)
-        # Note: For complex crates like wizer, we still need the existing "build" strategy
-        # The "source" strategy is primarily for avoiding ctx.execute() calls
-        wizer_path = "wizer_placeholder"
-
-        # Create placeholder since complex dependency resolution is challenging
-        ctx.file("wizer_placeholder", """#!/bin/bash
-echo "Wizer source strategy: Use 'build' or 'cargo' strategy for full functionality"
-echo "Source strategy eliminates ctx.execute calls but requires proper dependency resolution"
-exit 1
-""", executable = True)
-
-    elif strategy == "download":
-        # Download prebuilt binary from GitHub releases
-        platform_info = _get_wizer_download_info(platform, version)
-
-        # Download and extract the binary
-        ctx.download_and_extract(
-            url = platform_info["url"],
-            sha256 = platform_info["sha256"],
-            stripPrefix = platform_info["strip_prefix"],
-            type = platform_info["type"],
-        )
-
-        # The binary is now extracted directly to the root with the correct name
-        wizer_path = "wizer.exe" if "windows" in platform else "wizer"
-
-    else:
-        fail("Unsupported Wizer installation strategy: {}. Use 'build', 'cargo', 'source', or 'download'".format(strategy))
-
-    # Create BUILD file for the toolchain
-    if strategy == "build":
-        # For build strategy, reference the git repository
-        build_content = '''"""Wizer WebAssembly pre-initialization toolchain"""
-
-load("@rules_wasm_component//toolchains:wizer_toolchain.bzl", "wizer_toolchain")
-
-package(default_visibility = ["//visibility:public"])
-
-# Wizer executable from git repository (Bazel-native build)
-alias(
-    name = "wizer_bin",
-    actual = "@wizer_src//:wizer_bazel",
-    visibility = ["//visibility:public"],
-)
-'''
-    elif strategy == "source":
-        # For source strategy, use placeholder (avoids ctx.execute)
-        build_content = '''"""Wizer WebAssembly pre-initialization toolchain"""
-
-load("@rules_wasm_component//toolchains:wizer_toolchain.bzl", "wizer_toolchain")
-
-package(default_visibility = ["//visibility:public"])
-
-# Wizer placeholder (source strategy avoids ctx.execute calls)
-filegroup(
-    name = "wizer_bin",
-    srcs = ["{wizer_path}"],
-    visibility = ["//visibility:public"],
-)
-'''.format(wizer_path = wizer_path)
-    elif strategy == "download":
-        # For download strategy, use native file that's already executable
-        build_content = '''"""Wizer WebAssembly pre-initialization toolchain"""
-
-load("@rules_wasm_component//toolchains:wizer_toolchain.bzl", "wizer_toolchain")
-
-package(default_visibility = ["//visibility:public"])
-
-# Wizer executable (downloaded binary)
-sh_binary(
-    name = "wizer_bin",
-    srcs = ["{wizer_path}"],
-    visibility = ["//visibility:public"],
-)
-'''.format(wizer_path = wizer_path)
-    else:
-        # For other strategies, use local file
-        build_content = '''"""Wizer WebAssembly pre-initialization toolchain"""
-
-load("@rules_wasm_component//toolchains:wizer_toolchain.bzl", "wizer_toolchain")
-
-package(default_visibility = ["//visibility:public"])
-
-# Wizer executable
-filegroup(
-    name = "wizer_bin",
-    srcs = ["{wizer_path}"],
-)
-'''.format(wizer_path = wizer_path)
-
-    ctx.file("BUILD.bazel", build_content + '''
-# Wizer toolchain implementation
-wizer_toolchain(
-    name = "wizer_toolchain_impl",
-    wizer = "{wizer_path}",
-)
-
-# Toolchain definition
-toolchain(
-    name = "wizer_toolchain_def",
-    exec_compatible_with = [
-        "@platforms//os:{os}",
-        "@platforms//cpu:{cpu}",
-    ],
-    target_compatible_with = [
-        # Wizer runs on host platform to pre-initialize WASM modules
-    ],
-    toolchain = ":wizer_toolchain_impl",
-    toolchain_type = "@rules_wasm_component//toolchains:wizer_toolchain_type",
-    visibility = ["//visibility:public"],
-)
-'''.format(
-        wizer_path = wizer_path,
-        os = "osx" if "darwin" in platform else ("windows" if "windows" in platform else "linux"),
-        cpu = "arm64" if "arm64" in platform else "x86_64",
-    ))
-
-wizer_toolchain_repository = repository_rule(
-    implementation = _wizer_toolchain_repository_impl,
-    attrs = {
-        "bundle": attr.string(
-            default = "",
-            doc = "Toolchain bundle name. If set, version is read from checksums/toolchain_bundles.json",
-        ),
-        "version": attr.string(
-            default = "9.0.0",
-            doc = "Wizer version to install. Ignored if bundle is specified.",
-        ),
-        "strategy": attr.string(
-            default = "source",
-            values = ["build", "cargo", "source", "download"],
-            doc = "Installation strategy: 'build' (build from source), 'cargo' (install via cargo), 'source' (git repository), or 'download' (download prebuilt binary)",
-        ),
-    },
-    doc = "Repository rule for setting up Wizer toolchain",
-)
diff --git a/tools-builder/MODULE.bazel b/tools-builder/MODULE.bazel
index 2c6868b5..a76964a6 100644
--- a/tools-builder/MODULE.bazel
+++ b/tools-builder/MODULE.bazel
@@ -32,10 +32,10 @@ use_repo(rust, "rust_toolchains")
 register_toolchains("@rust_toolchains//:all")
 
 # External tool sources via git_repository
+# Note: wizer removed - now part of wasmtime v39.0.0+
 git_repos = use_extension("//toolchains:builder_extensions.bzl", "git_repos")
 git_repos.wasm_tools(tag = "v1.235.0")
 git_repos.wit_bindgen(tag = "v0.43.0")
-git_repos.wizer(tag = "v9.0.0")
 git_repos.wac(tag = "v0.7.0")
 git_repos.wasmtime(tag = "v35.0.0")
 use_repo(
@@ -44,7 +44,6 @@ use_repo(
     "wasm_tools_src",
     "wasmtime_src",
     "wit_bindgen_src",
-    "wizer_src",
 )
 
 # Rust crates for dependency management
diff --git a/tools-builder/toolchains/builder_extensions.bzl b/tools-builder/toolchains/builder_extensions.bzl
index d5e406b0..b5527662 100644
--- a/tools-builder/toolchains/builder_extensions.bzl
+++ b/tools-builder/toolchains/builder_extensions.bzl
@@ -25,14 +25,7 @@ def _git_repos_impl(module_ctx):
                 )
                 repos_created["wit_bindgen_src"] = True
 
-        for call in mod.tags.wizer:
-            if "wizer_src" not in repos_created:
-                module_ctx.download_and_extract(
-                    name = "wizer_src",
-                    url = "https://github.com/bytecodealliance/wizer/archive/refs/tags/{}.tar.gz".format(call.tag),
-                    strip_prefix = "wizer-{}".format(call.tag.lstrip("v")),
-                )
-                repos_created["wizer_src"] = True
+        # Note: wizer removed - now part of wasmtime v39.0.0+
 
         for call in mod.tags.wac:
             if "wac_src" not in repos_created:
@@ -61,10 +54,6 @@ _wit_bindgen_tag = tag_class(attrs = {
     "tag": attr.string(mandatory = True),
 })
 
-_wizer_tag = tag_class(attrs = {
-    "tag": attr.string(mandatory = True),
-})
-
 _wac_tag = tag_class(attrs = {
     "tag": attr.string(mandatory = True),
 })
@@ -79,7 +68,6 @@ git_repos = module_extension(
     tag_classes = {
         "wasm_tools": _wasm_tools_tag,
         "wit_bindgen": _wit_bindgen_tag,
-        "wizer": _wizer_tag,
         "wac": _wac_tag,
         "wasmtime": _wasmtime_tag,
     },
diff --git a/tools-builder/toolchains/builder_macros.bzl b/tools-builder/toolchains/builder_macros.bzl
index 0ace9aef..ec177cd9 100644
--- a/tools-builder/toolchains/builder_macros.bzl
+++ b/tools-builder/toolchains/builder_macros.bzl
@@ -38,13 +38,7 @@ def wasm_tool_suite(name, platforms, tools):
                     rust_target = platform_info["rust_target"],
                     suffix = platform_info["suffix"],
                 )
-            elif tool == "wizer":
-                _build_wizer(
-                    name = target_name,
-                    platform = platform,
-                    rust_target = platform_info["rust_target"],
-                    suffix = platform_info["suffix"],
-                )
+            # Note: wizer removed - now part of wasmtime v39.0.0+
             elif tool == "wac":
                 _build_wac(
                     name = target_name,
@@ -90,17 +84,6 @@ def _build_wit_bindgen(name, platform, rust_target, suffix):
         edition = "2021",
     )
 
-def _build_wizer(name, platform, rust_target, suffix):
-    """Build wizer for a specific platform"""
-    rust_binary(
-        name = name,
-        srcs = ["@wizer_src//:src/main.rs"],
-        deps = ["@wizer_src//:wizer_lib"],
-        platform = platform,
-        crate_name = "wizer",
-        edition = "2021",
-    )
-
 def _build_wac(name, platform, rust_target, suffix):
     """Build wac for a specific platform"""
     rust_binary(
diff --git a/tools-builder/tools/wizer/BUILD.bazel b/tools-builder/tools/wizer/BUILD.bazel
deleted file mode 100644
index 7c086c1a..00000000
--- a/tools-builder/tools/wizer/BUILD.bazel
+++ /dev/null
@@ -1,20 +0,0 @@
-"""BUILD file for wizer from source - simplified for tools-builder workspace"""
-
-load("@rules_rust//rust:defs.bzl", "rust_binary")
-
-package(default_visibility = ["//visibility:public"])
-
-# Simple wizer binary build for host platform only
-# This demonstrates the capability to build tools from source when downloads aren't available
-rust_binary(
-    name = "wizer",
-    srcs = ["@wizer_src//:src/bin/wizer.rs"],
-    crate_name = "wizer",
-    edition = "2021",
-    deps = [
-        "@crates//:anyhow",
-        "@crates//:clap",
-        # Additional dependencies would be added here as needed
-        # This is a minimal working example for CI validation
-    ],
-)
diff --git a/tools/checksum_updater/src/tool_config.rs b/tools/checksum_updater/src/tool_config.rs
index f0c61b29..0196f10b 100644
--- a/tools/checksum_updater/src/tool_config.rs
+++ b/tools/checksum_updater/src/tool_config.rs
@@ -208,9 +208,7 @@ impl ToolConfig {
             },
         );
 
-        // Note: wizer is in the JSON registry with valid checksums but
-        // has issues with GitHub API calls in the update engine, so we use
-        // the fallback checksum mechanism instead of auto-updates
+        // Note: wizer removed - now part of wasmtime v39.0.0+, use `wasmtime wizer` subcommand
 
         // wkg configuration
         tools.insert(
diff --git a/tools/wizer_initializer/BUILD.bazel b/tools/wizer_initializer/BUILD.bazel
deleted file mode 100644
index e42b14d3..00000000
--- a/tools/wizer_initializer/BUILD.bazel
+++ /dev/null
@@ -1,43 +0,0 @@
-"""Wizer library-based initializer tool and checksum updater"""
-
-load("@rules_rust//rust:defs.bzl", "rust_binary")
-
-package(default_visibility = ["//visibility:public"])
-
-# Simplified Wizer library placeholder demonstrating architecture
-# This version uses basic dependencies and serves as proof-of-concept
-rust_binary(
-    name = "wizer_initializer",
-    srcs = ["src/main.rs"],
-    edition = "2021",
-    deps = [
-        "@wizer_crates//:anyhow",
-        "@wizer_crates//:clap",
-    ],
-)
-
-# Checksum updater for automated SHA management
-rust_binary(
-    name = "checksum_updater",
-    srcs = ["src/checksum_updater.rs"],
-    edition = "2021",
-    deps = [
-        "@wizer_crates//:anyhow",
-        "@wizer_crates//:chrono",
-        "@wizer_crates//:clap",
-        "@wizer_crates//:futures-util",
-        "@wizer_crates//:octocrab",
-        "@wizer_crates//:reqwest",
-        "@wizer_crates//:serde",
-        "@wizer_crates//:serde_json",
-        "@wizer_crates//:sha2",
-        "@wizer_crates//:tempfile",
-        "@wizer_crates//:tokio",
-    ],
-)
-
-# Alias for easier command line usage
-alias(
-    name = "update_checksums",
-    actual = ":checksum_updater",
-)
diff --git a/tools/wizer_initializer/Cargo.lock b/tools/wizer_initializer/Cargo.lock
deleted file mode 100644
index 13401879..00000000
--- a/tools/wizer_initializer/Cargo.lock
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diff --git a/tools/wizer_initializer/Cargo.toml b/tools/wizer_initializer/Cargo.toml
deleted file mode 100644
index 9225cb1b..00000000
--- a/tools/wizer_initializer/Cargo.toml
+++ /dev/null
@@ -1,27 +0,0 @@
-[package]
-name = "wizer_initializer"
-version = "0.1.0"
-edition = "2021"
-
-[[bin]]
-name = "wizer_initializer"
-path = "src/main.rs"
-
-[[bin]]
-name = "checksum_updater"
-path = "src/checksum_updater.rs"
-
-[dependencies]
-anyhow = "1.0"
-clap = { version = "4.5.51", features = ["derive"] }
-
-# Additional dependencies for checksum updater
-reqwest = { version = "0.12", features = ["json", "stream"] }
-serde = { version = "1.0", features = ["derive"] }
-serde_json = "1.0"
-sha2 = "0.10"
-tokio = { version = "1.48", features = ["full"] }
-chrono = { version = "0.4", features = ["serde"] }
-futures-util = "0.3"
-tempfile = "3.23"
-octocrab = { version = "0.48.1", features = ["stream"] }
diff --git a/tools/wizer_initializer/src/checksum_updater.rs b/tools/wizer_initializer/src/checksum_updater.rs
deleted file mode 100644
index 89a328de..00000000
--- a/tools/wizer_initializer/src/checksum_updater.rs
+++ /dev/null
@@ -1,445 +0,0 @@
-use anyhow::{Context, Result};
-use chrono::{DateTime, Utc};
-use clap::{Arg, Command};
-use futures_util::StreamExt;
-use octocrab::{models::repos::Release, Octocrab};
-use serde::{Deserialize, Serialize};
-use sha2::{Digest, Sha256};
-use std::collections::HashMap;
-use std::fs;
-use std::path::Path;
-use tempfile::NamedTempFile;
-
-#[derive(Debug, Clone, Serialize, Deserialize)]
-struct PlatformInfo {
-    sha256: String,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    url_suffix: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    platform_name: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    binary_name: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    npm_package: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    npm_version: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    install_method: Option<String>,
-}
-
-#[derive(Debug, Clone, Serialize, Deserialize)]
-struct VersionInfo {
-    release_date: String,
-    platforms: HashMap<String, PlatformInfo>,
-}
-
-#[derive(Debug, Clone, Serialize, Deserialize)]
-struct ToolConfig {
-    tool_name: String,
-    github_repo: String,
-    latest_version: String,
-    last_checked: DateTime<Utc>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    note: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    install_method: Option<String>,
-    versions: HashMap<String, VersionInfo>,
-}
-
-#[derive(Debug, Clone)]
-struct ToolPattern {
-    name: String,
-    repo: String,
-    url_patterns: Vec<PlatformPattern>,
-    version_prefix: Option<String>,
-}
-
-#[derive(Debug, Clone)]
-struct PlatformPattern {
-    platform: String,
-    url_template: String,
-    additional_fields: HashMap<String, String>,
-}
-
-impl ToolPattern {
-    fn new(name: &str, repo: &str) -> Self {
-        Self {
-            name: name.to_string(),
-            repo: repo.to_string(),
-            url_patterns: vec![],
-            version_prefix: None,
-        }
-    }
-
-    fn with_version_prefix(mut self, prefix: &str) -> Self {
-        self.version_prefix = Some(prefix.to_string());
-        self
-    }
-
-    fn add_platform(mut self, platform: &str, url_template: &str) -> Self {
-        self.url_patterns.push(PlatformPattern {
-            platform: platform.to_string(),
-            url_template: url_template.to_string(),
-            additional_fields: HashMap::new(),
-        });
-        self
-    }
-
-    fn add_platform_with_fields(
-        mut self,
-        platform: &str,
-        url_template: &str,
-        fields: HashMap<String, String>,
-    ) -> Self {
-        self.url_patterns.push(PlatformPattern {
-            platform: platform.to_string(),
-            url_template: url_template.to_string(),
-            additional_fields: fields,
-        });
-        self
-    }
-}
-
-fn get_tool_patterns() -> Vec<ToolPattern> {
-    vec![
-        ToolPattern::new("wasm-tools", "bytecodealliance/wasm-tools")
-            .with_version_prefix("v")
-            .add_platform(
-                "darwin_amd64",
-                "https://github.com/bytecodealliance/wasm-tools/releases/download/v{version}/wasm-tools-{version}-x86_64-macos.tar.gz",
-            )
-            .add_platform(
-                "darwin_arm64",
-                "https://github.com/bytecodealliance/wasm-tools/releases/download/v{version}/wasm-tools-{version}-aarch64-macos.tar.gz",
-            )
-            .add_platform(
-                "linux_amd64",
-                "https://github.com/bytecodealliance/wasm-tools/releases/download/v{version}/wasm-tools-{version}-x86_64-linux.tar.gz",
-            )
-            .add_platform(
-                "linux_arm64",
-                "https://github.com/bytecodealliance/wasm-tools/releases/download/v{version}/wasm-tools-{version}-aarch64-linux.tar.gz",
-            )
-            .add_platform(
-                "windows_amd64",
-                "https://github.com/bytecodealliance/wasm-tools/releases/download/v{version}/wasm-tools-{version}-x86_64-windows.tar.gz",
-            ),
-        ToolPattern::new("wit-bindgen", "bytecodealliance/wit-bindgen")
-            .with_version_prefix("v")
-            .add_platform(
-                "darwin_amd64",
-                "https://github.com/bytecodealliance/wit-bindgen/releases/download/v{version}/wit-bindgen-{version}-x86_64-macos.tar.gz",
-            )
-            .add_platform(
-                "darwin_arm64",
-                "https://github.com/bytecodealliance/wit-bindgen/releases/download/v{version}/wit-bindgen-{version}-aarch64-macos.tar.gz",
-            )
-            .add_platform(
-                "linux_amd64",
-                "https://github.com/bytecodealliance/wit-bindgen/releases/download/v{version}/wit-bindgen-{version}-x86_64-linux.tar.gz",
-            )
-            .add_platform(
-                "linux_arm64",
-                "https://github.com/bytecodealliance/wit-bindgen/releases/download/v{version}/wit-bindgen-{version}-aarch64-linux.tar.gz",
-            )
-            .add_platform(
-                "windows_amd64",
-                "https://github.com/bytecodealliance/wit-bindgen/releases/download/v{version}/wit-bindgen-{version}-x86_64-windows.zip",
-            ),
-        ToolPattern::new("wasmtime", "bytecodealliance/wasmtime")
-            .with_version_prefix("v")
-            .add_platform(
-                "darwin_amd64",
-                "https://github.com/bytecodealliance/wasmtime/releases/download/v{version}/wasmtime-v{version}-x86_64-macos.tar.xz",
-            )
-            .add_platform(
-                "darwin_arm64",
-                "https://github.com/bytecodealliance/wasmtime/releases/download/v{version}/wasmtime-v{version}-aarch64-macos.tar.xz",
-            )
-            .add_platform(
-                "linux_amd64",
-                "https://github.com/bytecodealliance/wasmtime/releases/download/v{version}/wasmtime-v{version}-x86_64-linux.tar.xz",
-            )
-            .add_platform(
-                "linux_arm64",
-                "https://github.com/bytecodealliance/wasmtime/releases/download/v{version}/wasmtime-v{version}-aarch64-linux.tar.xz",
-            )
-            .add_platform(
-                "windows_amd64",
-                "https://github.com/bytecodealliance/wasmtime/releases/download/v{version}/wasmtime-v{version}-x86_64-windows.zip",
-            ),
-        ToolPattern::new("wac", "bytecodealliance/wac")
-            .with_version_prefix("v")
-            .add_platform_with_fields(
-                "darwin_amd64",
-                "https://github.com/bytecodealliance/wac/releases/download/v{version}/wac-cli-x86_64-apple-darwin",
-                [("platform_name".to_string(), "x86_64-apple-darwin".to_string())].into(),
-            )
-            .add_platform_with_fields(
-                "darwin_arm64",
-                "https://github.com/bytecodealliance/wac/releases/download/v{version}/wac-cli-aarch64-apple-darwin",
-                [("platform_name".to_string(), "aarch64-apple-darwin".to_string())].into(),
-            )
-            .add_platform_with_fields(
-                "linux_amd64",
-                "https://github.com/bytecodealliance/wac/releases/download/v{version}/wac-cli-x86_64-unknown-linux-musl",
-                [("platform_name".to_string(), "x86_64-unknown-linux-musl".to_string())].into(),
-            )
-            .add_platform_with_fields(
-                "linux_arm64",
-                "https://github.com/bytecodealliance/wac/releases/download/v{version}/wac-cli-aarch64-unknown-linux-musl",
-                [("platform_name".to_string(), "aarch64-unknown-linux-musl".to_string())].into(),
-            )
-            .add_platform_with_fields(
-                "windows_amd64",
-                "https://github.com/bytecodealliance/wac/releases/download/v{version}/wac-cli-x86_64-pc-windows-gnu",
-                [("platform_name".to_string(), "x86_64-pc-windows-gnu".to_string())].into(),
-            ),
-    ]
-}
-
-async fn fetch_latest_release(github: &Octocrab, repo: &str) -> Result<Release> {
-    let (owner, repo_name) = repo
-        .split_once('/')
-        .context("Invalid repository format. Expected 'owner/repo'")?;
-
-    github
-        .repos(owner, repo_name)
-        .releases()
-        .get_latest()
-        .await
-        .context("Failed to fetch latest release")
-}
-
-async fn download_and_hash(url: &str) -> Result<String> {
-    println!("Downloading and hashing: {}", url);
-
-    let response = reqwest::get(url).await.context("Failed to download file")?;
-
-    if !response.status().is_success() {
-        anyhow::bail!("Download failed with status: {}", response.status());
-    }
-
-    let mut hasher = Sha256::new();
-    let mut stream = response.bytes_stream();
-
-    while let Some(chunk) = stream.next().await {
-        let chunk = chunk.context("Failed to read chunk")?;
-        hasher.update(&chunk);
-    }
-
-    let hash = hasher.finalize();
-    Ok(format!("{:x}", hash))
-}
-
-async fn update_tool_checksums(
-    checksums_dir: &Path,
-    tool_pattern: &ToolPattern,
-    dry_run: bool,
-) -> Result<bool> {
-    println!("Checking tool: {}", tool_pattern.name);
-
-    let github = Octocrab::builder().build()?;
-    let latest_release = fetch_latest_release(&github, &tool_pattern.repo).await?;
-
-    let version = latest_release.tag_name.clone();
-    let clean_version = if let Some(prefix) = &tool_pattern.version_prefix {
-        version.strip_prefix(prefix).unwrap_or(&version)
-    } else {
-        &version
-    };
-
-    println!("Latest version: {} (clean: {})", version, clean_version);
-
-    let config_path = checksums_dir
-        .join("tools")
-        .join(format!("{}.json", tool_pattern.name));
-    let mut config: ToolConfig = if config_path.exists() {
-        let content = fs::read_to_string(&config_path)?;
-        serde_json::from_str(&content)?
-    } else {
-        ToolConfig {
-            tool_name: tool_pattern.name.clone(),
-            github_repo: tool_pattern.repo.clone(),
-            latest_version: clean_version.to_string(),
-            last_checked: Utc::now(),
-            note: None,
-            install_method: None,
-            versions: HashMap::new(),
-        }
-    };
-
-    // Check if we already have this version
-    if config.versions.contains_key(clean_version) {
-        println!("Version {} already exists, skipping", clean_version);
-        // Update last_checked time
-        config.last_checked = Utc::now();
-        if !dry_run {
-            let updated_content = serde_json::to_string_pretty(&config)?;
-            fs::write(&config_path, updated_content)?;
-        }
-        return Ok(false);
-    }
-
-    println!(
-        "New version {} found, calculating checksums...",
-        clean_version
-    );
-
-    let mut platforms = HashMap::new();
-    for platform_pattern in &tool_pattern.url_patterns {
-        let url = platform_pattern
-            .url_template
-            .replace("{version}", clean_version);
-
-        match download_and_hash(&url).await {
-            Ok(checksum) => {
-                println!("✅ {}: {}", platform_pattern.platform, checksum);
-
-                let mut platform_info = PlatformInfo {
-                    sha256: checksum,
-                    url_suffix: None,
-                    platform_name: None,
-                    binary_name: None,
-                    npm_package: None,
-                    npm_version: None,
-                    install_method: None,
-                };
-
-                // Add additional fields based on tool pattern
-                for (key, value) in &platform_pattern.additional_fields {
-                    match key.as_str() {
-                        "platform_name" => platform_info.platform_name = Some(value.clone()),
-                        "binary_name" => platform_info.binary_name = Some(value.clone()),
-                        "url_suffix" => platform_info.url_suffix = Some(value.clone()),
-                        _ => {}
-                    }
-                }
-
-                // Infer url_suffix from URL if not provided
-                if platform_info.url_suffix.is_none() {
-                    if let Some(suffix) = url.split('/').last() {
-                        if let Some(tool_and_suffix) = suffix
-                            .strip_prefix(&format!("{}-{}-", tool_pattern.name, clean_version))
-                        {
-                            platform_info.url_suffix = Some(tool_and_suffix.to_string());
-                        } else if suffix.contains(&tool_pattern.name) {
-                            // For wasmtime format: wasmtime-v{version}-{platform}.tar.xz
-                            if let Some(platform_suffix) =
-                                suffix.split(&format!("v{}-", clean_version)).nth(1)
-                            {
-                                platform_info.url_suffix = Some(platform_suffix.to_string());
-                            }
-                        }
-                    }
-                }
-
-                platforms.insert(platform_pattern.platform.clone(), platform_info);
-            }
-            Err(e) => {
-                println!("❌ Failed to download {}: {}", platform_pattern.platform, e);
-            }
-        }
-    }
-
-    if platforms.is_empty() {
-        println!("❌ No platforms successfully processed");
-        return Ok(false);
-    }
-
-    // Add new version to config
-    config.versions.insert(
-        clean_version.to_string(),
-        VersionInfo {
-            release_date: latest_release
-                .published_at
-                .map(|dt| dt.format("%Y-%m-%d").to_string())
-                .unwrap_or_else(|| Utc::now().format("%Y-%m-%d").to_string()),
-            platforms,
-        },
-    );
-
-    config.latest_version = clean_version.to_string();
-    config.last_checked = Utc::now();
-
-    if !dry_run {
-        let updated_content = serde_json::to_string_pretty(&config)?;
-        fs::write(&config_path, updated_content)?;
-        println!("✅ Updated {}", config_path.display());
-    } else {
-        println!("🔍 Would update {}", config_path.display());
-    }
-
-    Ok(true)
-}
-
-#[tokio::main]
-async fn main() -> Result<()> {
-    let matches = Command::new("Checksum Updater")
-        .version("1.0")
-        .about("Updates tool checksums by checking GitHub releases")
-        .arg(
-            Arg::new("checksums-dir")
-                .long("checksums-dir")
-                .value_name("DIR")
-                .help("Path to checksums directory")
-                .default_value("checksums"),
-        )
-        .arg(
-            Arg::new("tool")
-                .long("tool")
-                .value_name("TOOL")
-                .help("Update specific tool only"),
-        )
-        .arg(
-            Arg::new("dry-run")
-                .long("dry-run")
-                .help("Show what would be updated without making changes")
-                .action(clap::ArgAction::SetTrue),
-        )
-        .get_matches();
-
-    let checksums_dir = Path::new(matches.get_one::<String>("checksums-dir").unwrap());
-    let specific_tool = matches.get_one::<String>("tool");
-    let dry_run = matches.get_flag("dry-run");
-
-    if !checksums_dir.exists() {
-        anyhow::bail!(
-            "Checksums directory does not exist: {}",
-            checksums_dir.display()
-        );
-    }
-
-    let tool_patterns = get_tool_patterns();
-    let mut any_updates = false;
-
-    for tool_pattern in tool_patterns {
-        if let Some(tool_filter) = specific_tool {
-            if tool_pattern.name != *tool_filter {
-                continue;
-            }
-        }
-
-        match update_tool_checksums(checksums_dir, &tool_pattern, dry_run).await {
-            Ok(updated) => {
-                if updated {
-                    any_updates = true;
-                }
-            }
-            Err(e) => {
-                eprintln!("❌ Failed to update {}: {}", tool_pattern.name, e);
-            }
-        }
-    }
-
-    if any_updates {
-        println!("\n✅ Tool checksums updated successfully!");
-        if !dry_run {
-            println!("💡 Remember to test the updated checksums and commit the changes.");
-        }
-    } else {
-        println!("\n📅 All tools are up to date.");
-    }
-
-    Ok(())
-}
diff --git a/tools/wizer_initializer/src/main.rs b/tools/wizer_initializer/src/main.rs
deleted file mode 100644
index f7616825..00000000
--- a/tools/wizer_initializer/src/main.rs
+++ /dev/null
@@ -1,186 +0,0 @@
-use anyhow::{Context, Result};
-use clap::Parser;
-use std::fs;
-use std::path::PathBuf;
-
-#[derive(Parser, Debug)]
-#[command(
-    name = "wizer_initializer",
-    about = "WebAssembly pre-initialization using Wizer library",
-    version
-)]
-struct Args {
-    /// Input WebAssembly component file
-    #[arg(short, long)]
-    input: PathBuf,
-
-    /// Output pre-initialized WebAssembly component file
-    #[arg(short, long)]
-    output: PathBuf,
-
-    /// Name of the initialization function to call
-    #[arg(long, default_value = "wizer.initialize")]
-    init_func: String,
-
-    /// Allow WASI calls during initialization
-    #[arg(long)]
-    allow_wasi: bool,
-
-    /// Inherit stdio during initialization
-    #[arg(long)]
-    inherit_stdio: bool,
-
-    /// Enable verbose output
-    #[arg(short, long)]
-    verbose: bool,
-}
-
-fn main() -> Result<()> {
-    let args = Args::parse();
-
-    if args.verbose {
-        eprintln!("Wizer Initializer starting...");
-        eprintln!("Input: {:?}", args.input);
-        eprintln!("Output: {:?}", args.output);
-        eprintln!("Init function: {}", args.init_func);
-    }
-
-    // Read the input WebAssembly file
-    let input_bytes = fs::read(&args.input)
-        .with_context(|| format!("Failed to read input file: {:?}", args.input))?;
-
-    if args.verbose {
-        eprintln!("Read {} bytes from input file", input_bytes.len());
-    }
-
-    // Check if this is a WebAssembly component or module
-    let is_component = is_wasm_component(&input_bytes)?;
-
-    if args.verbose {
-        eprintln!(
-            "Input is a WebAssembly {}",
-            if is_component { "component" } else { "module" }
-        );
-    }
-
-    // Extract the core module from the component if needed
-    let core_module_bytes = if is_component {
-        if args.verbose {
-            eprintln!("Extracting core module from component...");
-        }
-        extract_core_module(&input_bytes)
-            .with_context(|| "Failed to extract core module from component")?
-    } else {
-        input_bytes.clone()
-    };
-
-    if args.verbose {
-        eprintln!("Core module size: {} bytes", core_module_bytes.len());
-    }
-
-    // Apply Wizer pre-initialization to the core module
-    if args.verbose {
-        eprintln!("Running Wizer pre-initialization placeholder...");
-        eprintln!("Would call Wizer with init_func: {}", args.init_func);
-        eprintln!("Would set allow_wasi: {}", args.allow_wasi);
-        eprintln!("Would set inherit_stdio: {}", args.inherit_stdio);
-    }
-
-    // PLACEHOLDER: In a full implementation, this would use Wizer library
-    // let mut wizer = wizer::Wizer::new();
-    // wizer.init_func(&args.init_func);
-    // if args.allow_wasi { wizer.allow_wasi(true); }
-    // if args.inherit_stdio { wizer.inherit_stdio(true); }
-    // let initialized_module_bytes = wizer.run(&core_module_bytes)?;
-
-    eprintln!("WARNING: Wizer pre-initialization not yet implemented - returning input as-is");
-    let initialized_module_bytes = core_module_bytes;
-
-    if args.verbose {
-        eprintln!(
-            "Pre-initialization complete. Output size: {} bytes",
-            initialized_module_bytes.len()
-        );
-    }
-
-    // If the input was a component, we need to wrap the initialized module back into a component
-    let final_output_bytes = if is_component {
-        if args.verbose {
-            eprintln!("Wrapping initialized module back into component...");
-        }
-        wrap_module_as_component(&initialized_module_bytes)
-            .with_context(|| "Failed to wrap module as component")?
-    } else {
-        initialized_module_bytes
-    };
-
-    // Write the output file
-    fs::write(&args.output, &final_output_bytes)
-        .with_context(|| format!("Failed to write output file: {:?}", args.output))?;
-
-    if args.verbose {
-        eprintln!(
-            "Successfully wrote {} bytes to {:?}",
-            final_output_bytes.len(),
-            args.output
-        );
-    }
-
-    println!(
-        "Pre-initialization complete: {:?} -> {:?}",
-        args.input, args.output
-    );
-
-    Ok(())
-}
-
-/// Check if the given bytes represent a WebAssembly component (vs module)
-fn is_wasm_component(bytes: &[u8]) -> Result<bool> {
-    if bytes.len() < 8 {
-        return Ok(false);
-    }
-
-    // Check WebAssembly magic number
-    if &bytes[0..4] != b"\0asm" {
-        return Ok(false);
-    }
-
-    // Check version - components use different version encoding
-    let version_bytes = &bytes[4..8];
-    let version = u32::from_le_bytes([
-        version_bytes[0],
-        version_bytes[1],
-        version_bytes[2],
-        version_bytes[3],
-    ]);
-
-    // Version 0x1000d indicates a component
-    Ok(version == 0x1000d)
-}
-
-/// Extract the core WebAssembly module from a component
-/// This is a simplified implementation - in production, you'd use proper component parsing
-fn extract_core_module(component_bytes: &[u8]) -> Result<Vec<u8>> {
-    // PLACEHOLDER: In a full implementation, this would use wasm-tools or wasmtime
-    // to parse the component and extract the core module
-
-    eprintln!("WARNING: Component parsing not yet implemented - using placeholder approach");
-
-    // For now, just return the input bytes - this demonstrates the architecture
-    // In production, this would call:
-    // wasm-tools component wit <component> --core-module
-    Ok(component_bytes.to_vec())
-}
-
-/// Wrap a WebAssembly module as a component
-/// This is a simplified implementation - in production, you'd use proper component tooling
-fn wrap_module_as_component(module_bytes: &[u8]) -> Result<Vec<u8>> {
-    // This is a placeholder that would use wasm-tools or similar to wrap
-    // the module as a component. For now, we'll just return the module.
-
-    // In a full implementation, this would use something like:
-    // wasm-tools component new <module> -o <component>
-
-    eprintln!("Warning: Component wrapping not yet implemented. Returning module as-is.");
-    Ok(module_bytes.to_vec())
-}
diff --git a/wasm/extensions.bzl b/wasm/extensions.bzl
index cd11788b..b4e536de 100644
--- a/wasm/extensions.bzl
+++ b/wasm/extensions.bzl
@@ -6,7 +6,6 @@ load("//toolchains:tinygo_toolchain.bzl", "tinygo_toolchain_repository")
 load("//toolchains:wasi_sdk_toolchain.bzl", "wasi_sdk_repository")
 load("//toolchains:wasm_toolchain.bzl", "wasm_toolchain_repository")
 load("//toolchains:wasmtime_toolchain.bzl", "wasmtime_repository")
-load("//toolchains:wizer_toolchain.bzl", "wizer_toolchain_repository")
 load("//toolchains:wkg_toolchain.bzl", "wkg_toolchain_repository")
 load("//wit:wasi_deps.bzl", "wasi_wit_dependencies")
 
@@ -47,20 +46,13 @@ def _wasm_component_bundle_impl(module_ctx):
         strategy = "download",
     )
 
-    # Wasmtime runtime
+    # Wasmtime runtime (includes wizer as of v39.0.0)
     wasmtime_repository(
         name = "wasmtime_toolchain",
         bundle = bundle_name,
         strategy = "download",
     )
 
-    # Wizer pre-initialization
-    wizer_toolchain_repository(
-        name = "wizer_toolchain",
-        bundle = bundle_name,
-        strategy = "download",
-    )
-
     # WKG package manager
     wkg_toolchain_repository(
         name = "wkg_toolchain",
@@ -125,7 +117,7 @@ combinations from checksums/toolchain_bundles.json.
 Example:
     wasm_bundle = use_extension("@rules_wasm_component//wasm:extensions.bzl", "wasm_component_bundle")
     wasm_bundle.configure(bundle = "stable-2025-12")
-    use_repo(wasm_bundle, "wasm_tools_toolchains", "wasmtime_toolchain", "wizer_toolchain", ...)
+    use_repo(wasm_bundle, "wasm_tools_toolchains", "wasmtime_toolchain", ...)
 """,
 )
 
@@ -486,55 +478,8 @@ tinygo = module_extension(
     },
 )
 
-def _wizer_extension_impl(module_ctx):
-    """Implementation of Wizer module extension"""
-
-    registrations = {}
-
-    # Collect all Wizer registrations
-    for mod in module_ctx.modules:
-        for registration in mod.tags.register:
-            registrations[registration.name] = registration
-
-    # Create Wizer repositories
-    for name, registration in registrations.items():
-        wizer_toolchain_repository(
-            name = name + "_toolchain",
-            version = registration.version,
-            strategy = registration.strategy,
-        )
-
-    # If no registrations, create default Wizer toolchain
-    if not registrations:
-        wizer_toolchain_repository(
-            name = "wizer_toolchain",
-            version = "9.0.0",
-            strategy = "download",
-        )
-
-# Module extension for Wizer WebAssembly pre-initialization
-wizer = module_extension(
-    implementation = _wizer_extension_impl,
-    tag_classes = {
-        "register": tag_class(
-            attrs = {
-                "name": attr.string(
-                    doc = "Name for this Wizer registration",
-                    default = "wizer",
-                ),
-                "version": attr.string(
-                    doc = "Wizer version to install",
-                    default = "9.0.0",
-                ),
-                "strategy": attr.string(
-                    doc = "Installation strategy: 'download' (download prebuilt binary from GitHub releases)",
-                    default = "download",
-                    values = ["download"],
-                ),
-            },
-        ),
-    },
-)
+# Note: Standalone wizer extension removed - wizer is now part of wasmtime v39.0.0+
+# Use wasmtime extension below and invoke via `wasmtime wizer` subcommand
 
 def _wasmtime_extension_impl(module_ctx):
     """Implementation of Wasmtime module extension"""
diff --git a/wasm/wasm_component_wizer.bzl b/wasm/wasm_component_wizer.bzl
index ece9afe5..c750f7da 100644
--- a/wasm/wasm_component_wizer.bzl
+++ b/wasm/wasm_component_wizer.bzl
@@ -1,49 +1,55 @@
-"""Wizer pre-initialization rule for WebAssembly components"""
+"""Wizer pre-initialization rule for WebAssembly components.
+
+As of Wasmtime v39.0.0 (November 2025), the standalone Wizer tool has been
+merged upstream into Wasmtime. This rule now uses `wasmtime wizer` subcommand
+instead of the standalone wizer binary for better maintenance and component
+model support.
+
+See: https://github.com/bytecodealliance/wasmtime/releases/tag/v39.0.0
+"""
 
 def _wasm_component_wizer_impl(ctx):
-    """Implementation of wasm_component_wizer rule"""
+    """Implementation of wasm_component_wizer rule using wasmtime wizer subcommand"""
 
-    # Get Wizer toolchain
-    wizer_toolchain = ctx.toolchains["//toolchains:wizer_toolchain_type"]
-    wizer = wizer_toolchain.wizer
+    # Get Wasmtime toolchain (wizer is now part of wasmtime)
+    wasmtime_toolchain = ctx.toolchains["//toolchains:wasmtime_toolchain_type"]
+    wasmtime = wasmtime_toolchain.wasmtime
 
     # Input and output files
     input_wasm = ctx.file.component
     output_wasm = ctx.outputs.wizer_component
 
-    # Create initialization script if provided
-    init_script = None
-    if ctx.attr.init_script:
-        init_script = ctx.file.init_script
-
-    # Build Wizer command arguments
+    # Build wasmtime wizer command arguments
+    # Format: wasmtime wizer [OPTIONS] <INPUT> -o <OUTPUT>
     args = ctx.actions.args()
+    args.add("wizer")  # wasmtime subcommand
     args.add("--allow-wasi")  # Allow WASI imports during initialization
-    args.add("--inherit-stdio", "true")  # Inherit stdio for debugging if needed
 
     # Add custom initialization function name if specified
+    # Note: As of wasmtime v39.0.0, the default function name changed from
+    # "wizer.initialize" to "wizer-initialize" for better component compatibility
     if ctx.attr.init_function_name:
         args.add("--init-func", ctx.attr.init_function_name)
     else:
-        args.add("--init-func", "wizer.initialize")  # Default function name
+        args.add("--init-func", "wizer-initialize")  # New default function name
 
-    # Add input and output files
+    # Add output file
     args.add("-o", output_wasm.path)
+
+    # Add input file
     args.add(input_wasm.path)
 
     # Create action inputs list
     inputs = [input_wasm]
-    if init_script:
-        inputs.append(init_script)
 
-    # Run Wizer pre-initialization
+    # Run wasmtime wizer pre-initialization
     ctx.actions.run(
-        executable = wizer,
+        executable = wasmtime,
         arguments = [args],
         inputs = inputs,
         outputs = [output_wasm],
-        mnemonic = "WizerPreInit",
-        progress_message = "Pre-initializing WebAssembly component with Wizer: {}".format(
+        mnemonic = "WasmtimeWizer",
+        progress_message = "Pre-initializing WebAssembly component with wasmtime wizer: {}".format(
             input_wasm.short_path,
         ),
         use_default_shell_env = False,
@@ -72,32 +78,35 @@ wasm_component_wizer = rule(
             doc = "Input WebAssembly component to pre-initialize",
         ),
         "init_function_name": attr.string(
-            default = "wizer.initialize",
-            doc = "Name of the initialization function to call (default: wizer.initialize)",
-        ),
-        "init_script": attr.label(
-            allow_single_file = True,
-            doc = "Optional initialization script or data file",
+            default = "wizer-initialize",
+            doc = "Name of the initialization function to call (default: wizer-initialize). " +
+                  "Note: Prior to wasmtime v39.0.0, the default was 'wizer.initialize'.",
         ),
     },
     outputs = {
         "wizer_component": "%{name}_wizer.wasm",
     },
-    toolchains = ["//toolchains:wizer_toolchain_type"],
-    doc = """Pre-initialize a WebAssembly component with Wizer.
+    toolchains = ["//toolchains:wasmtime_toolchain_type"],
+    doc = """Pre-initialize a WebAssembly component with wasmtime wizer.
 
     This rule takes a WebAssembly component and runs Wizer pre-initialization on it,
     which can provide 1.35-6x startup performance improvements by running initialization
     code at build time rather than runtime.
 
-    The input component must export a function named 'wizer.initialize' (or the name
+    As of Wasmtime v39.0.0 (November 2025), the standalone Wizer tool has been merged
+    upstream into Wasmtime. This rule uses the `wasmtime wizer` subcommand.
+
+    The input component must export a function named 'wizer-initialize' (or the name
     specified in init_function_name) that performs the initialization work.
 
+    Note: The default init function name changed from 'wizer.initialize' to
+    'wizer-initialize' in wasmtime v39.0.0 for better component model compatibility.
+
     Example:
         wasm_component_wizer(
             name = "optimized_component",
             component = ":my_component",
-            init_function_name = "wizer.initialize",
+            init_function_name = "wizer-initialize",
         )
     """,
 )
@@ -116,33 +125,35 @@ def _wizer_chain_impl(ctx):
 
     component_file = original_files[0]
 
-    # Get Wizer initializer tool (handles Component → Module → Wizer → Component)
-    wizer_initializer = ctx.executable._wizer_initializer
+    # Get Wasmtime toolchain (wizer is now part of wasmtime as of v39.0.0)
+    wasmtime_toolchain = ctx.toolchains["//toolchains:wasmtime_toolchain_type"]
+    wasmtime = wasmtime_toolchain.wasmtime
 
     # Output file
     output_wasm = ctx.outputs.wizer_component
 
-    # Build Wizer initializer arguments
+    # Build wasmtime wizer arguments
     args = ctx.actions.args()
-    args.add("--input", component_file.path)
-    args.add("--output", output_wasm.path)
+    args.add("wizer")  # wasmtime subcommand
     args.add("--allow-wasi")
-    args.add("--inherit-stdio")
-    args.add("--verbose")
 
     if ctx.attr.init_function_name:
         args.add("--init-func", ctx.attr.init_function_name)
     else:
-        args.add("--init-func", "wizer_initialize")
+        args.add("--init-func", "wizer-initialize")
+
+    # Add output and input
+    args.add("-o", output_wasm.path)
+    args.add(component_file.path)
 
-    # Run Wizer initializer (Component → Module → Wizer → Component)
+    # Run wasmtime wizer
     ctx.actions.run(
-        executable = wizer_initializer,
+        executable = wasmtime,
         arguments = [args],
         inputs = [component_file],
         outputs = [output_wasm],
-        mnemonic = "WizerChain",
-        progress_message = "Wizer pre-initializing component (via initializer): {}".format(ctx.label.name),
+        mnemonic = "WasmtimeWizerChain",
+        progress_message = "Wizer pre-initializing component: {}".format(ctx.label.name),
         use_default_shell_env = False,
         env = {"RUST_BACKTRACE": "1"},
     )
@@ -162,23 +173,21 @@ wizer_chain = rule(
             doc = "WebAssembly component target to pre-initialize",
         ),
         "init_function_name": attr.string(
-            default = "wizer_initialize",
-            doc = "Name of the initialization function",
-        ),
-        "_wizer_initializer": attr.label(
-            default = "//tools/wizer_initializer:wizer_initializer",
-            executable = True,
-            cfg = "exec",
-            doc = "Wizer initializer tool for Component → Module → Wizer → Component workflow",
+            default = "wizer-initialize",
+            doc = "Name of the initialization function (default: wizer-initialize)",
         ),
     },
     outputs = {
         "wizer_component": "%{name}_wizer.wasm",
     },
+    toolchains = ["//toolchains:wasmtime_toolchain_type"],
     doc = """Chain Wizer pre-initialization after an existing component rule.
 
     This is a convenience rule that takes the output of another component-building
-    rule and applies Wizer pre-initialization to it.
+    rule and applies Wizer pre-initialization to it using wasmtime wizer.
+
+    As of Wasmtime v39.0.0 (November 2025), the standalone Wizer tool has been merged
+    upstream into Wasmtime. This rule uses the `wasmtime wizer` subcommand.
 
     Example:
         go_wasm_component(
diff --git a/wasm/wasm_component_wizer_library.bzl b/wasm/wasm_component_wizer_library.bzl
index 4b080ea6..719c22a5 100644
--- a/wasm/wasm_component_wizer_library.bzl
+++ b/wasm/wasm_component_wizer_library.bzl
@@ -1,35 +1,43 @@
-"""Wizer library-based pre-initialization rule for WebAssembly components"""
+"""Wizer pre-initialization rule for WebAssembly components.
+
+As of Wasmtime v39.0.0 (November 2025), the standalone Wizer tool has been
+merged upstream into Wasmtime. This rule uses `wasmtime wizer` subcommand
+for proper component model support.
+
+See: https://github.com/bytecodealliance/wasmtime/releases/tag/v39.0.0
+"""
 
 def _wasm_component_wizer_library_impl(ctx):
-    """Implementation using Wizer library for proper component model support"""
+    """Implementation using wasmtime wizer for proper component model support"""
 
     # Input and output files
     input_wasm = ctx.file.component
     output_wasm = ctx.outputs.wizer_component
 
-    # Get the wizer_initializer tool
-    wizer_initializer = ctx.executable._wizer_initializer
+    # Get Wasmtime toolchain (wizer is now part of wasmtime as of v39.0.0)
+    wasmtime_toolchain = ctx.toolchains["//toolchains:wasmtime_toolchain_type"]
+    wasmtime = wasmtime_toolchain.wasmtime
 
-    # Build command arguments
+    # Build wasmtime wizer command arguments
     args = ctx.actions.args()
-    args.add("--input", input_wasm)
-    args.add("--output", output_wasm)
+    args.add("wizer")  # wasmtime subcommand
     args.add("--init-func", ctx.attr.init_function_name)
 
     if ctx.attr.allow_wasi:
         args.add("--allow-wasi")
 
-    if ctx.attr.verbose:
-        args.add("--verbose")
+    # Add output and input
+    args.add("-o", output_wasm.path)
+    args.add(input_wasm.path)
 
-    # Run the wizer library initializer
+    # Run wasmtime wizer
     ctx.actions.run(
-        executable = wizer_initializer,
+        executable = wasmtime,
         arguments = [args],
         inputs = [input_wasm],
         outputs = [output_wasm],
-        mnemonic = "WizerLibraryInit",
-        progress_message = "Pre-initializing WebAssembly component with Wizer library: {}".format(
+        mnemonic = "WasmtimeWizerLib",
+        progress_message = "Pre-initializing WebAssembly component with wasmtime wizer: {}".format(
             input_wasm.short_path,
         ),
         use_default_shell_env = False,
@@ -58,8 +66,9 @@ wasm_component_wizer_library = rule(
             doc = "Input WebAssembly component to pre-initialize",
         ),
         "init_function_name": attr.string(
-            default = "wizer.initialize",
-            doc = "Name of the initialization function to call (default: wizer.initialize)",
+            default = "wizer-initialize",
+            doc = "Name of the initialization function to call (default: wizer-initialize). " +
+                  "Note: Prior to wasmtime v39.0.0, the default was 'wizer.initialize'.",
         ),
         "allow_wasi": attr.bool(
             default = True,
@@ -67,34 +76,32 @@ wasm_component_wizer_library = rule(
         ),
         "verbose": attr.bool(
             default = False,
-            doc = "Enable verbose output",
-        ),
-        "_wizer_initializer": attr.label(
-            default = "//tools/wizer_initializer:wizer_initializer",
-            executable = True,
-            cfg = "exec",
+            doc = "Enable verbose output (currently unused, kept for API compatibility)",
         ),
     },
     outputs = {
         "wizer_component": "%{name}_wizer.wasm",
     },
-    doc = """Pre-initialize a WebAssembly component using Wizer library.
+    toolchains = ["//toolchains:wasmtime_toolchain_type"],
+    doc = """Pre-initialize a WebAssembly component using wasmtime wizer.
 
-    This rule uses Wizer as a library (rather than CLI tool) to properly handle
-    WebAssembly components. The workflow is:
+    This rule uses wasmtime's built-in wizer subcommand to properly handle
+    WebAssembly components with full component model support.
 
-    1. Parse component to extract core module
-    2. Apply Wizer pre-initialization to the core module
-    3. Wrap the initialized module back as a component
+    As of Wasmtime v39.0.0 (November 2025), the standalone Wizer tool has been
+    merged upstream into Wasmtime, providing better maintenance and integration.
 
     This approach provides proper component model support and integrates well
     with Wasmtime runtime for initialization.
 
+    Note: The default init function name changed from 'wizer.initialize' to
+    'wizer-initialize' in wasmtime v39.0.0 for better component model compatibility.
+
     Example:
         wasm_component_wizer_library(
             name = "optimized_component",
             component = ":my_component",
-            init_function_name = "wizer.initialize",
+            init_function_name = "wizer-initialize",
             allow_wasi = True,
         )
     """,