diff --git a/packages/backend-app-api/src/wiring/BackendInitializer.ts b/packages/backend-app-api/src/wiring/BackendInitializer.ts
index 2f3a11b7e0..ee62ef966d 100644
--- a/packages/backend-app-api/src/wiring/BackendInitializer.ts
+++ b/packages/backend-app-api/src/wiring/BackendInitializer.ts
@@ -148,24 +148,6 @@ function createRootInstanceMetadataServiceFactory(
   });
 }
 
-function createDeprecatedInstanceMetadataServiceFactory() {
-  return createServiceFactory({
-    service: instanceMetadataServiceRef,
-    deps: {
-      instanceMetadata: coreServices.rootInstanceMetadata,
-    },
-    factory: async ({ instanceMetadata }) => {
-      const plugins = await instanceMetadata.getInstalledPlugins();
-      const service = {
-        getInstalledFeatures: () =>
-          plugins.map(e => ({ type: 'plugin' as const, pluginId: e.pluginId })),
-      };
-
-      return service;
-    },
-  });
-}
-
 export class BackendInitializer {
   #startPromise?: Promise<void>;
   #stopPromise?: Promise<void>;
@@ -269,7 +251,6 @@ export class BackendInitializer {
     this.#serviceRegistry.add(
       createRootInstanceMetadataServiceFactory(this.#registrations),
     );
-    this.#serviceRegistry.add(createDeprecatedInstanceMetadataServiceFactory());
 
     // This makes sure that any uncaught errors or unhandled rejections are
     // caught and logged, rather than terminating the process. We register these
diff --git a/packages/backend-defaults/src/CreateBackend.ts b/packages/backend-defaults/src/CreateBackend.ts
index 4b201fded3..44df59b5f1 100644
--- a/packages/backend-defaults/src/CreateBackend.ts
+++ b/packages/backend-defaults/src/CreateBackend.ts
@@ -38,6 +38,7 @@ import { eventsServiceFactory } from '@backstage/plugin-events-node';
 import {
   actionsRegistryServiceFactory,
   actionsServiceFactory,
+  instanceMetadataServiceFactory,
 } from '@backstage/backend-defaults/alpha';
 
 export const defaultServiceFactories = [
@@ -65,6 +66,7 @@ export const defaultServiceFactories = [
   // alpha services
   actionsRegistryServiceFactory,
   actionsServiceFactory,
+  instanceMetadataServiceFactory,
 ];
 
 /**
diff --git a/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/index.ts b/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/index.ts
new file mode 100644
index 0000000000..00ee75400a
--- /dev/null
+++ b/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/index.ts
@@ -0,0 +1,17 @@
+/*
+ * Copyright 2025 The Backstage Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+export { instanceMetadataServiceFactory } from './instanceMetadataServiceFactory';
diff --git a/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.ts b/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.ts
new file mode 100644
index 0000000000..f5e3af503b
--- /dev/null
+++ b/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.ts
@@ -0,0 +1,37 @@
+/*
+ * Copyright 2025 The Backstage Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import {
+  coreServices,
+  createServiceFactory,
+} from '@backstage/backend-plugin-api';
+import { instanceMetadataServiceRef } from '@backstage/backend-plugin-api/alpha';
+
+export const instanceMetadataServiceFactory = createServiceFactory({
+  service: instanceMetadataServiceRef,
+  deps: {
+    instanceMetadata: coreServices.rootInstanceMetadata,
+  },
+  factory: async ({ instanceMetadata }) => {
+    const plugins = await instanceMetadata.getInstalledPlugins();
+    const service = {
+      getInstalledFeatures: () =>
+        plugins.map(e => ({ type: 'plugin' as const, pluginId: e.pluginId })),
+    };
+
+    return service;
+  },
+});
diff --git a/packages/backend-defaults/src/alpha/index.ts b/packages/backend-defaults/src/alpha/index.ts
index 13bb439acd..744d5bc552 100644
--- a/packages/backend-defaults/src/alpha/index.ts
+++ b/packages/backend-defaults/src/alpha/index.ts
@@ -15,3 +15,4 @@
  */
 export { actionsRegistryServiceFactory } from './entrypoints/actionsRegistry';
 export { actionsServiceFactory } from './entrypoints/actions';
+export { instanceMetadataServiceFactory } from './entrypoints/instanceMetadata';
diff --git a/packages/backend-test-utils/src/services/mockServices.ts b/packages/backend-test-utils/src/services/mockServices.ts
index 2782724d11..9ecb59a35b 100644
--- a/packages/backend-test-utils/src/services/mockServices.ts
+++ b/packages/backend-test-utils/src/services/mockServices.ts
@@ -34,7 +34,7 @@ import {
   DatabaseService,
   DiscoveryService,
   HttpAuthService,
-  InstanceMetadataService,
+  RootInstanceMetadataService,
   LoggerService,
   PermissionsService,
   RootConfigService,
@@ -558,18 +558,18 @@ export namespace mockServices {
     }));
   }
 
-  export function instanceMetadata(): InstanceMetadataService {
+  export function rootInstanceMetadata(): RootInstanceMetadataService {
     return {
       getInstalledPlugins: () => Promise.resolve([]),
     };
   }
-  export namespace instanceMetadata {
-    export const mock = simpleMock(coreServices.instanceMetadata, () => ({
+  export namespace rootInstanceMetadata {
+    export const mock = simpleMock(coreServices.rootInstanceMetadata, () => ({
       getInstalledPlugins: jest.fn(),
     }));
     export const factory = simpleFactoryWithOptions(
-      coreServices.instanceMetadata,
-      instanceMetadata,
+      coreServices.rootInstanceMetadata,
+      rootInstanceMetadata,
     );
   }
 }