diff --git a/.changeset/four-peaches-train.md b/.changeset/four-peaches-train.md
new file mode 100644
index 0000000000..81b35589c1
--- /dev/null
+++ b/.changeset/four-peaches-train.md
@@ -0,0 +1,6 @@
+---
+'@backstage/backend-defaults': patch
+'@backstage/backend-plugin-api': patch
+---
+
+**BREAKING ALPHA**: The old `instanceMetadataService` has been removed from alpha. Please switch over to using the stable `coreServices.rootInstanceMetadata` and related types instead, available from `@backstage/backend-plugin-api`.
diff --git a/packages/backend-defaults/report-alpha.api.md b/packages/backend-defaults/report-alpha.api.md
index 2ca3525946..58277b5e1e 100644
--- a/packages/backend-defaults/report-alpha.api.md
+++ b/packages/backend-defaults/report-alpha.api.md
@@ -5,7 +5,6 @@
 ```ts
 import { ActionsRegistryService } from '@backstage/backend-plugin-api/alpha';
 import { ActionsService } from '@backstage/backend-plugin-api/alpha';
-import { InstanceMetadataService } from '@backstage/backend-plugin-api/alpha';
 import { ServiceFactory } from '@backstage/backend-plugin-api';
 
 // @public (undocumented)
@@ -22,12 +21,5 @@ export const actionsServiceFactory: ServiceFactory<
   'singleton'
 >;
 
-// @alpha @deprecated (undocumented)
-export const instanceMetadataServiceFactory: ServiceFactory<
-  InstanceMetadataService,
-  'plugin',
-  'singleton'
->;
-
 // (No @packageDocumentation comment for this package)
 ```
diff --git a/packages/backend-defaults/src/CreateBackend.ts b/packages/backend-defaults/src/CreateBackend.ts
index 44df59b5f1..9f8116a996 100644
--- a/packages/backend-defaults/src/CreateBackend.ts
+++ b/packages/backend-defaults/src/CreateBackend.ts
@@ -38,8 +38,8 @@ import { eventsServiceFactory } from '@backstage/plugin-events-node';
 import {
   actionsRegistryServiceFactory,
   actionsServiceFactory,
-  instanceMetadataServiceFactory,
 } from '@backstage/backend-defaults/alpha';
+import { instanceMetadataServiceFactory } from './alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory';
 
 export const defaultServiceFactories = [
   auditorServiceFactory,
@@ -66,6 +66,8 @@ export const defaultServiceFactories = [
   // alpha services
   actionsRegistryServiceFactory,
   actionsServiceFactory,
+
+  // Unexported alpha services kept around for compatibility reasons
   instanceMetadataServiceFactory,
 ];
 
diff --git a/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/index.ts b/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/index.ts
deleted file mode 100644
index 00ee75400a..0000000000
--- a/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/index.ts
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * 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.test.ts b/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.test.ts
index 2368ea74e8..73de60efdd 100644
--- a/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.test.ts
+++ b/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.test.ts
@@ -18,9 +18,11 @@ import {
   coreServices,
   createBackendPlugin,
 } from '@backstage/backend-plugin-api';
-import { instanceMetadataServiceFactory } from './instanceMetadataServiceFactory';
+import {
+  instanceMetadataServiceFactory,
+  instanceMetadataServiceRef,
+} from './instanceMetadataServiceFactory';
 import { startTestBackend } from '@backstage/backend-test-utils';
-import { instanceMetadataServiceRef } from '@backstage/backend-plugin-api/alpha';
 import Router from 'express-promise-router';
 import request from 'supertest';
 
diff --git a/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.ts b/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.ts
index bd2d427a59..eb50037511 100644
--- a/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.ts
+++ b/packages/backend-defaults/src/alpha/entrypoints/instanceMetadata/instanceMetadataServiceFactory.ts
@@ -17,16 +17,46 @@
 import {
   coreServices,
   createServiceFactory,
+  createServiceRef,
 } from '@backstage/backend-plugin-api';
-import {
-  BackendFeatureMeta,
-  InstanceMetadataService,
-  instanceMetadataServiceRef,
-} from '@backstage/backend-plugin-api/alpha';
+
+/*
+ * NOTE(freben): We have moved over to coreServices.rootInstanceMetadata. This
+ * old alpha implementation is kept around for a little longer for backward
+ * compatibility reasons.
+ */
 
 /**
- * @alpha
- * @deprecated use {@link @backstage/backend-plugin-api#coreServices.rootInstanceMetadata} instead
+ * @internal
+ */
+export type BackendFeatureMeta =
+  | {
+      type: 'plugin';
+      pluginId: string;
+    }
+  | {
+      type: 'module';
+      pluginId: string;
+      moduleId: string;
+    };
+
+/**
+ * @internal
+ */
+export interface InstanceMetadataService {
+  getInstalledFeatures: () => BackendFeatureMeta[];
+}
+
+/**
+ * @internal
+ */
+export const instanceMetadataServiceRef =
+  createServiceRef<InstanceMetadataService>({
+    id: 'core.instanceMetadata',
+  });
+
+/**
+ * @internal
  */
 export const instanceMetadataServiceFactory = createServiceFactory({
   service: instanceMetadataServiceRef,
diff --git a/packages/backend-defaults/src/alpha/index.ts b/packages/backend-defaults/src/alpha/index.ts
index 744d5bc552..da63aef9de 100644
--- a/packages/backend-defaults/src/alpha/index.ts
+++ b/packages/backend-defaults/src/alpha/index.ts
@@ -13,6 +13,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+
 export { actionsRegistryServiceFactory } from './entrypoints/actionsRegistry';
 export { actionsServiceFactory } from './entrypoints/actions';
-export { instanceMetadataServiceFactory } from './entrypoints/instanceMetadata';
diff --git a/packages/backend-plugin-api/report-alpha.api.md b/packages/backend-plugin-api/report-alpha.api.md
index 9be7a29ed5..cefed593c0 100644
--- a/packages/backend-plugin-api/report-alpha.api.md
+++ b/packages/backend-plugin-api/report-alpha.api.md
@@ -103,30 +103,5 @@ export const actionsServiceRef: ServiceRef<
   'singleton'
 >;
 
-// @alpha (undocumented)
-export type BackendFeatureMeta =
-  | {
-      type: 'plugin';
-      pluginId: string;
-    }
-  | {
-      type: 'module';
-      pluginId: string;
-      moduleId: string;
-    };
-
-// @alpha (undocumented)
-export interface InstanceMetadataService {
-  // (undocumented)
-  getInstalledFeatures: () => BackendFeatureMeta[];
-}
-
-// @alpha (undocumented)
-export const instanceMetadataServiceRef: ServiceRef<
-  InstanceMetadataService,
-  'plugin',
-  'singleton'
->;
-
 // (No @packageDocumentation comment for this package)
 ```
diff --git a/packages/backend-plugin-api/src/alpha/InstanceMetadataService.ts b/packages/backend-plugin-api/src/alpha/InstanceMetadataService.ts
deleted file mode 100644
index a82a261d9d..0000000000
--- a/packages/backend-plugin-api/src/alpha/InstanceMetadataService.ts
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * 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.
- */
-
-/** @alpha */
-export type BackendFeatureMeta =
-  | {
-      type: 'plugin';
-      pluginId: string;
-    }
-  | {
-      type: 'module';
-      pluginId: string;
-      moduleId: string;
-    };
-
-/** @alpha */
-export interface InstanceMetadataService {
-  getInstalledFeatures: () => BackendFeatureMeta[];
-}
diff --git a/packages/backend-plugin-api/src/alpha/index.ts b/packages/backend-plugin-api/src/alpha/index.ts
index 5bb69eb4e2..b1edd68adc 100644
--- a/packages/backend-plugin-api/src/alpha/index.ts
+++ b/packages/backend-plugin-api/src/alpha/index.ts
@@ -14,11 +14,6 @@
  * limitations under the License.
  */
 
-export type {
-  BackendFeatureMeta,
-  InstanceMetadataService,
-} from './InstanceMetadataService';
-
 export type {
   ActionsRegistryService,
   ActionsRegistryActionOptions,
@@ -27,8 +22,4 @@ export type {
 
 export type { ActionsService, ActionsServiceAction } from './ActionsService';
 
-export {
-  actionsRegistryServiceRef,
-  actionsServiceRef,
-  instanceMetadataServiceRef,
-} from './refs';
+export { actionsRegistryServiceRef, actionsServiceRef } from './refs';
diff --git a/packages/backend-plugin-api/src/alpha/refs.ts b/packages/backend-plugin-api/src/alpha/refs.ts
index 81996679f7..cfbb215615 100644
--- a/packages/backend-plugin-api/src/alpha/refs.ts
+++ b/packages/backend-plugin-api/src/alpha/refs.ts
@@ -16,15 +16,6 @@
 
 import { createServiceRef } from '@backstage/backend-plugin-api';
 
-/**
- * @alpha
- */
-export const instanceMetadataServiceRef = createServiceRef<
-  import('./InstanceMetadataService').InstanceMetadataService
->({
-  id: 'core.instanceMetadata',
-});
-
 /**
  * Service for calling distributed actions
  *