diff --git a/packages/frontend-app-api/src/wiring/createSpecializedApp.test.tsx b/packages/frontend-app-api/src/wiring/createSpecializedApp.test.tsx
index f954ba5750..8a4e2b5c9b 100644
--- a/packages/frontend-app-api/src/wiring/createSpecializedApp.test.tsx
+++ b/packages/frontend-app-api/src/wiring/createSpecializedApp.test.tsx
@@ -16,6 +16,7 @@
 
 import {
   AppTreeApi,
+  type ApiRef,
   appTreeApiRef,
   coreExtensionData,
   createExtension,
@@ -422,6 +423,64 @@ describe('createSpecializedApp', () => {
     expect(app.apis.get(testApiRef)).toEqual({ value: 'owner' });
   });
 
+  it('should ignore plugin ownership metadata from unsupported opaque ApiRefs', () => {
+    const testApiRef = {
+      $$type: '@backstage/ApiRef',
+      version: 'v0',
+      id: 'shared.api',
+      pluginId: 'owner',
+      T: null as unknown as { value: string },
+      toString() {
+        return 'apiRef{shared.api}';
+      },
+    } as ApiRef<{ value: string }, 'shared.api'> & {
+      readonly $$type: '@backstage/ApiRef';
+      readonly version: 'v0';
+      readonly pluginId: 'owner';
+    };
+
+    const app = createSpecializedApp({
+      features: [
+        makeAppPlugin(),
+        createFrontendPlugin({
+          pluginId: 'other-before',
+          extensions: [
+            ApiBlueprint.make({
+              params: defineParams =>
+                defineParams({
+                  api: testApiRef,
+                  deps: {},
+                  factory: () => ({ value: 'other' }),
+                }),
+            }),
+          ],
+        }),
+        createFrontendPlugin({
+          pluginId: 'owner',
+          extensions: [
+            ApiBlueprint.make({
+              params: defineParams =>
+                defineParams({
+                  api: testApiRef,
+                  deps: {},
+                  factory: () => ({ value: 'owner' }),
+                }),
+            }),
+          ],
+        }),
+      ],
+    });
+
+    expect(app.errors).toEqual([
+      expect.objectContaining({
+        code: 'API_FACTORY_CONFLICT',
+        message: expect.stringContaining("API 'shared.api'"),
+      }),
+    ]);
+
+    expect(app.apis.get(testApiRef)).toEqual({ value: 'other' });
+  });
+
   it('should not infer app ownership from core-prefixed API ids', () => {
     const testApiRef = createApiRef<{ value: string }>({ id: 'core.shared' });
 
diff --git a/packages/frontend-app-api/src/wiring/createSpecializedApp.tsx b/packages/frontend-app-api/src/wiring/createSpecializedApp.tsx
index fd009db479..20c00c8929 100644
--- a/packages/frontend-app-api/src/wiring/createSpecializedApp.tsx
+++ b/packages/frontend-app-api/src/wiring/createSpecializedApp.tsx
@@ -51,6 +51,8 @@ import {
   resolveExtensionDefinition,
   toInternalExtension,
 } from '../../../frontend-plugin-api/src/wiring/resolveExtensionDefinition';
+// eslint-disable-next-line @backstage/no-relative-monorepo-imports
+import { OpaqueApiRef } from '../../../frontend-plugin-api/src/apis/system/ApiRef';
 
 import {
   extractRouteInfoFromAppNode,
@@ -456,9 +458,15 @@ function createApiFactories(options: {
 // TODO(Rugvip): It would be good if this was more explicit, but I think that
 //               might need to wait for some future update for API factories.
 function getApiOwnerId(apiRef: { id: string }): string {
-  const pluginId = (apiRef as { pluginId?: string }).pluginId;
-  if (pluginId) {
-    return pluginId;
+  if (OpaqueApiRef.isType(apiRef)) {
+    try {
+      const { pluginId } = OpaqueApiRef.toInternal(apiRef);
+      if (pluginId) {
+        return pluginId;
+      }
+    } catch {
+      // Fall back to legacy ID inference for unsupported opaque ApiRef versions.
+    }
   }
 
   const apiRefId = apiRef.id;
diff --git a/packages/frontend-plugin-api/src/apis/system/ApiRef.ts b/packages/frontend-plugin-api/src/apis/system/ApiRef.ts
index 15f10874fc..2d86f0a8ad 100644
--- a/packages/frontend-plugin-api/src/apis/system/ApiRef.ts
+++ b/packages/frontend-plugin-api/src/apis/system/ApiRef.ts
@@ -31,12 +31,14 @@ type ApiRefBuilderConfig<TId extends string> = {
   pluginId?: string;
 };
 
-const OpaqueApiRef = OpaqueType.create<{
+/** @internal */
+export const OpaqueApiRef = OpaqueType.create<{
   public: ApiRef<unknown> & {
     readonly $$type: '@backstage/ApiRef';
   };
   versions: {
     readonly version: 'v1';
+    readonly pluginId?: string;
   };
 }>({
   type: '@backstage/ApiRef',