diff --git a/packages/compiler/native/ts7-process.test.c b/packages/compiler/native/ts7-process.test.c
index b6d760abd..85de63db1 100644
--- a/packages/compiler/native/ts7-process.test.c
+++ b/packages/compiler/native/ts7-process.test.c
@@ -1,6 +1,10 @@
 #ifndef _WIN32
 #define _POSIX_C_SOURCE 200809L
 #endif
+/* macOS declares mkdtemp only with the Darwin extensions visible. */
+#if defined(__APPLE__) && !defined(_DARWIN_C_SOURCE)
+#define _DARWIN_C_SOURCE 1
+#endif
 #include "ts7-process.h"
 #include <assert.h>
 #include <errno.h>
diff --git a/packages/compiler/src/backend/native-toolchain.test.ts b/packages/compiler/src/backend/native-toolchain.test.ts
index f1bcde404..0ac21e853 100644
--- a/packages/compiler/src/backend/native-toolchain.test.ts
+++ b/packages/compiler/src/backend/native-toolchain.test.ts
@@ -24,6 +24,7 @@ import {
   compileLibArchive,
   executableSectionEliminationFlags,
   executableNativeEnvironmentFingerprint,
+  implicitDependencyIncludeDirective,
   implicitDependencyProbeIncludes,
   parseLinkTraceFiles,
   resolveBuildCacheRoot,
@@ -624,6 +625,46 @@ test("implicit dependency seeds include separately compiled vendor system header
   expect(includes).toContain("<stdatomic.h>");
 });
 
+test.skipIf(clangExecutable === undefined)(
+  "the implicit toolchain probe guards target-specific compiler headers",
+  async () => {
+    // clang ships its x86 intrinsic headers (<emmintrin.h>, ...) for every
+    // target, so __has_include finds them on arm64, where including them is
+    // an #error, and the same holds for the ARM headers on x86. The probe
+    // must guard them by target. Only the compiler's own freestanding
+    // headers are visible here, so the result does not depend on the host's
+    // C library.
+    const includes = (await implicitDependencyProbeIncludes(runtimeSrcDir())).filter(
+      (include) =>
+        include !== "<intrin.h>" && /intrin\.h>$|^<cpuid\.h>$|^<arm_(neon|acle)\.h>$/.test(include),
+    );
+    expect(includes).toContain("<emmintrin.h>");
+    const resourceDir = execFileSync(clangExecutable!, ["-print-resource-dir"], {
+      encoding: "utf8",
+    }).trim();
+    const source = includes.map(implicitDependencyIncludeDirective).join("");
+    for (const target of ["aarch64-unknown-linux-gnu", "x86_64-unknown-linux-gnu"]) {
+      const result = spawnSync(
+        clangExecutable!,
+        [
+          `--target=${target}`,
+          "-ffreestanding",
+          "-nostdinc",
+          "-isystem",
+          join(resourceDir, "include"),
+          "-fsyntax-only",
+          "-x",
+          "c",
+          "-",
+        ],
+        { input: source, encoding: "utf8" },
+      );
+      expect(result.stderr, target).toBe("");
+      expect(result.status, target).toBe(0);
+    }
+  },
+);
+
 test.skipIf(
   process.platform === "win32" ||
     clangExecutable === undefined ||
diff --git a/packages/compiler/src/backend/native-toolchain.ts b/packages/compiler/src/backend/native-toolchain.ts
index 05f1f7122..6c024c6a5 100644
--- a/packages/compiler/src/backend/native-toolchain.ts
+++ b/packages/compiler/src/backend/native-toolchain.ts
@@ -26,7 +26,10 @@ export {
 export { CcCompileError, subprocessFailureDetail } from "./native/process.js";
 export { compileLibArchive } from "./native/library.js";
 export { localizeLibraryObjects } from "./native/object-merge.js";
-export { implicitDependencyProbeIncludes } from "./native/compiler-fingerprint.js";
+export {
+  implicitDependencyIncludeDirective,
+  implicitDependencyProbeIncludes,
+} from "./native/compiler-fingerprint.js";
 export { parseLinkTraceFiles, nativeLinkerDependencyPaths } from "./native/linker-fingerprint.js";
 export { clearCcCaches, stageRuntimeObjects } from "./native/runtime-objects.js";
 export {
diff --git a/packages/compiler/src/backend/native/compiler-fingerprint.ts b/packages/compiler/src/backend/native/compiler-fingerprint.ts
index ec427ce0a..6f92707f6 100644
--- a/packages/compiler/src/backend/native/compiler-fingerprint.ts
+++ b/packages/compiler/src/backend/native/compiler-fingerprint.ts
@@ -195,15 +195,25 @@ export async function implicitDependencyProbeIncludes(rtDir: string): Promise<st
   return [...includes].sort();
 }
 
-function implicitDependencyIncludeDirective(include: string): string {
-  const targetCondition =
-    include === "<cpuid.h>" || include === "<immintrin.h>"
-      ? " && (defined(__i386__) || defined(__x86_64__) || defined(_M_IX86) || defined(_M_X64))"
-      : include === "<intrin.h>"
-        ? " && defined(_WIN32)"
-        : include === "<arm64_neon.h>" || include === "<arm_acle.h>" || include === "<arm_neon.h>"
-          ? " && (defined(__arm__) || defined(__aarch64__) || defined(_M_ARM) || defined(_M_ARM64))"
-          : "";
+/** Compiler-provided x86 headers: clang ships them for every target, so
+ * __has_include finds them on arm64 too, where including them is an
+ * #error. Covers the SSE/AVX intrinsic families (<emmintrin.h>,
+ * <immintrin.h>, ...), <x86intrin.h>, <x86gprintrin.h> and <cpuid.h>. */
+function x86OnlyHeader(include: string): boolean {
+  return include === "<cpuid.h>" || /^<(x86|x86gpr|[a-z]*mm)intrin\.h>$/.test(include);
+}
+
+/** One guarded line of the implicit-toolchain probe source: the header is
+ * included only when the compiler can find it and it belongs to the target
+ * being probed. */
+export function implicitDependencyIncludeDirective(include: string): string {
+  const targetCondition = x86OnlyHeader(include)
+    ? " && (defined(__i386__) || defined(__x86_64__) || defined(_M_IX86) || defined(_M_X64))"
+    : include === "<intrin.h>"
+      ? " && defined(_WIN32)"
+      : include === "<arm64_neon.h>" || include === "<arm_acle.h>" || include === "<arm_neon.h>"
+        ? " && (defined(__arm__) || defined(__aarch64__) || defined(_M_ARM) || defined(_M_ARM64))"
+        : "";
   return `#if __has_include(${include})${targetCondition}\n#include ${include}\n#endif\n`;
 }