diff --git a/src/dotnet/ManagedArtifactInspector.test.ts b/src/dotnet/ManagedArtifactInspector.test.ts
index 3b734c176..50de3a39b 100644
--- a/src/dotnet/ManagedArtifactInspector.test.ts
+++ b/src/dotnet/ManagedArtifactInspector.test.ts
@@ -547,6 +547,63 @@ describe("managed fixture data layout", () => {
   });
 });
 
+describe("managed implementation classification", () => {
+  it("classifies crossgen2 ReadyToRun output without ILONLY as modern .NET", () => {
+    // crossgen2 writes IL_LIBRARY | STRONGNAMESIGNED and clears ILONLY.
+    const bytes = buildManagedPeFixture({ readyToRun: true, cliFlags: 0xc });
+    const result = inspectManagedArtifactBytes(
+      bytes,
+      managedPeFixtureTarget(bytes),
+    );
+
+    expect(result.classification).toMatchObject({
+      runtime_family: "modern-dotnet",
+      implementation: "cil-and-ready-to-run",
+    });
+    expect(result.classification.evidence).toContainEqual(
+      expect.objectContaining({ code: "ready-to-run-signature-observed" }),
+    );
+    expect(result.classification.evidence).not.toContainEqual(
+      expect.objectContaining({ code: "cli-il-only-clear" }),
+    );
+  });
+
+  it("preserves ReadyToRun runtime identity after metadata capacity is exhausted", () => {
+    const bytes = buildManagedPeFixture({
+      readyToRun: true,
+      cliFlags: 0xc,
+      references: ["x".repeat(12 * 1024 * 1024)],
+    });
+    const result = inspectManagedArtifactBytes(
+      bytes,
+      managedPeFixtureTarget(bytes),
+    );
+    expect(result.classification).toMatchObject({
+      status: "managed",
+      runtime_family: "modern-dotnet",
+    });
+    expect(result.coverage.issues).toContainEqual(
+      expect.objectContaining({ code: "resource-limit" }),
+    );
+  });
+
+  it("keeps a clear ILONLY flag without ReadyToRun as mixed CLR/native", () => {
+    const bytes = buildManagedPeFixture({ cliFlags: 0 });
+    const result = inspectManagedArtifactBytes(
+      bytes,
+      managedPeFixtureTarget(bytes),
+    );
+
+    expect(result.classification).toMatchObject({
+      runtime_family: "mixed-clr-native",
+      implementation: "cpp-cli-mixed",
+    });
+    expect(result.classification.evidence).toContainEqual(
+      expect.objectContaining({ code: "cli-il-only-clear" }),
+    );
+  });
+});
+
 describe("managed artifact metadata identity", () => {
   it("accepts CLI metadata GUIDs without RFC UUID version or variant bits", () => {
     const bytes = buildManagedPeFixture({
diff --git a/src/dotnet/ManagedArtifactInspector.ts b/src/dotnet/ManagedArtifactInspector.ts
index 7e7acb087..625969aba 100644
--- a/src/dotnet/ManagedArtifactInspector.ts
+++ b/src/dotnet/ManagedArtifactInspector.ts
@@ -158,6 +158,15 @@ interface RuntimeClassificationInput {
   readonly inventory: ManagedMetadataInventory;
 }
 
+const runtimeFamilyFromCliHeader = (
+  cli: ManagedCliHeader | null,
+): ManagedArtifactInspection["classification"]["runtime_family"] =>
+  cli?.readyToRunSignature === true
+    ? "modern-dotnet"
+    : cli !== null && (cli.flags & 1) === 0
+      ? "mixed-clr-native"
+      : "unknown";
+
 const runtimeFamilyFor = (
   cli: ManagedCliHeader,
   inventory: ManagedMetadataInventory,
@@ -180,7 +189,9 @@ const runtimeFamilyFor = (
   );
   let runtimeFamily: ManagedArtifactInspection["classification"]["runtime_family"] =
     "unknown";
-  if ((cli.flags & 1) === 0) {
+  // crossgen2 clears ILONLY on ReadyToRun output, so only a clear flag
+  // without the ReadyToRun signature indicates mixed CLR/native code.
+  if (runtimeFamilyFromCliHeader(cli) === "mixed-clr-native") {
     runtimeFamily = "mixed-clr-native";
     evidence.push({
       code: "cli-il-only-clear",
@@ -239,8 +250,8 @@ const implementationFor = (
   cli: ManagedCliHeader,
   metadata: ManagedMetadataLayout,
 ): ManagedArtifactInspection["classification"]["implementation"] => {
-  if ((cli.flags & 1) === 0) return "cpp-cli-mixed";
   if (cli.readyToRunSignature) return "cil-and-ready-to-run";
+  if ((cli.flags & 1) === 0) return "cpp-cli-mixed";
   return (metadata.rowCounts[6] ?? 0) === 0 ? "metadata-only" : "cil";
 };
 
@@ -303,8 +314,7 @@ const partialMetadataResult = ({
   classification: {
     status: issue.code === "resource-limit" ? "managed" : "malformed",
     container: "pe",
-    runtime_family:
-      (layout.cli?.flags ?? 1) & 1 ? "unknown" : "mixed-clr-native",
+    runtime_family: runtimeFamilyFromCliHeader(layout.cli),
     implementation: "unknown",
     managed_architecture: "unknown",
     evidence: [