diff --git a/.changeset/breezy-flowers-dance.md b/.changeset/breezy-flowers-dance.md
new file mode 100644
index 0000000000..51bd9db5f1
--- /dev/null
+++ b/.changeset/breezy-flowers-dance.md
@@ -0,0 +1,5 @@
+---
+'@backstage/backend-app-api': patch
+---
+
+Deprecate the `featureDiscoveryServiceFactory` in favor of using `featureDiscoveryLoader` instead.
diff --git a/.changeset/calm-brooms-fail.md b/.changeset/calm-brooms-fail.md
new file mode 100644
index 0000000000..d99a479d93
--- /dev/null
+++ b/.changeset/calm-brooms-fail.md
@@ -0,0 +1,5 @@
+---
+'@backstage/backend-dynamic-feature-service': patch
+---
+
+Deprecate the `dynamicPluginsServiceRef`, `dynamicPluginsServiceFactory` and `dynamicPluginsServiceFactoryWithOptions` in favor of using `dynamicPluginsFeatureDiscoveryLoader` or `dynamicPluginsFeatureDiscoveryLoaderWithOptions` instead.
diff --git a/.changeset/fuzzy-mails-walk.md b/.changeset/fuzzy-mails-walk.md
new file mode 100644
index 0000000000..d00d372415
--- /dev/null
+++ b/.changeset/fuzzy-mails-walk.md
@@ -0,0 +1,5 @@
+---
+'@backstage/backend-plugin-api': patch
+---
+
+Deprecate the `featureDiscoveryServiceRef` in favor of using `@backstage/backend-app-api#featureDiscoveryLoader` instead.
diff --git a/packages/backend-app-api/api-report-alpha.md b/packages/backend-app-api/api-report-alpha.md
index 2633321472..8ff4e61390 100644
--- a/packages/backend-app-api/api-report-alpha.md
+++ b/packages/backend-app-api/api-report-alpha.md
@@ -3,10 +3,14 @@
 > Do not edit this file. It is a report generated by [API Extractor](https://api-extractor.com/).
 
 ```ts
+import { BackendFeature } from '@backstage/backend-plugin-api';
 import { FeatureDiscoveryService } from '@backstage/backend-plugin-api/alpha';
 import { ServiceFactory } from '@backstage/backend-plugin-api';
 
-// @alpha (undocumented)
+// @public
+export const featureDiscoveryLoader: BackendFeature;
+
+// @alpha @deprecated (undocumented)
 export const featureDiscoveryServiceFactory: ServiceFactory<
   FeatureDiscoveryService,
   'root',
diff --git a/packages/backend-app-api/src/alpha.ts b/packages/backend-app-api/src/alpha.ts
index a334214738..41bf4950d4 100644
--- a/packages/backend-app-api/src/alpha.ts
+++ b/packages/backend-app-api/src/alpha.ts
@@ -14,4 +14,7 @@
  * limitations under the License.
  */
 
-export { featureDiscoveryServiceFactory } from './alpha/featureDiscoveryServiceFactory';
+export {
+  featureDiscoveryLoader,
+  featureDiscoveryServiceFactory,
+} from './alpha/featureDiscoveryServiceFactory';
diff --git a/packages/backend-app-api/src/alpha/featureDiscoveryServiceFactory.ts b/packages/backend-app-api/src/alpha/featureDiscoveryServiceFactory.ts
index c16a3f6534..e901f0c367 100644
--- a/packages/backend-app-api/src/alpha/featureDiscoveryServiceFactory.ts
+++ b/packages/backend-app-api/src/alpha/featureDiscoveryServiceFactory.ts
@@ -19,6 +19,7 @@ import {
   RootConfigService,
   RootLoggerService,
   coreServices,
+  createBackendFeatureLoader,
   createServiceFactory,
 } from '@backstage/backend-plugin-api';
 import {
@@ -153,7 +154,10 @@ class PackageDiscoveryService implements FeatureDiscoveryService {
   }
 }
 
-/** @alpha */
+/**
+ * @alpha
+ * @deprecated The `featureDiscoveryServiceFactory` is deprecated in favor of using {@link featureDiscoveryLoader} instead.
+ */
 export const featureDiscoveryServiceFactory = createServiceFactory({
   service: featureDiscoveryServiceRef,
   deps: {
@@ -165,6 +169,36 @@ export const featureDiscoveryServiceFactory = createServiceFactory({
   },
 });
 
+/**
+ * A loader that discovers backend features from the current package.json and its dependencies.
+ *
+ * @public
+ *
+ * @example
+ * Using the `featureDiscoveryLoader` loader in a backend instance:
+ * ```ts
+ * //...
+ * import { createBackend } from '@backstage/backend-defaults';
+ * import { featureDiscoveryLoader } from '@backstage/backend-app-api';
+ *
+ * const backend = createBackend();
+ * backend.add(featureDiscoveryLoader);
+ * //...
+ * backend.start();
+ * ```
+ */
+export const featureDiscoveryLoader = createBackendFeatureLoader({
+  deps: {
+    config: coreServices.rootConfig,
+    logger: coreServices.rootLogger,
+  },
+  async loader({ config, logger }) {
+    const service = new PackageDiscoveryService(config, logger);
+    const { features } = await service.getBackendFeatures();
+    return features;
+  },
+});
+
 function isBackendFeature(value: unknown): value is BackendFeature {
   return (
     !!value &&
diff --git a/packages/backend-app-api/src/wiring/BackendInitializer.test.ts b/packages/backend-app-api/src/wiring/BackendInitializer.test.ts
index 955e463bb0..65fc21ccde 100644
--- a/packages/backend-app-api/src/wiring/BackendInitializer.test.ts
+++ b/packages/backend-app-api/src/wiring/BackendInitializer.test.ts
@@ -20,32 +20,23 @@ import { loggerServiceFactory } from '@backstage/backend-defaults/logger';
 import {
   createServiceRef,
   createServiceFactory,
-  coreServices,
   createBackendPlugin,
   createBackendModule,
   createExtensionPoint,
   createBackendFeatureLoader,
 } from '@backstage/backend-plugin-api';
 import { BackendInitializer } from './BackendInitializer';
+import { mockServices } from '@backstage/backend-test-utils';
 
-class MockLogger {
-  debug() {}
-  info() {}
-  warn() {}
-  error() {}
-  child() {
-    return this;
-  }
-}
+const requiredRootFactories = [
+  mockServices.rootConfig.factory(),
+  mockServices.rootLogger.factory(),
+];
 
 const baseFactories = [
+  ...requiredRootFactories,
   lifecycleServiceFactory,
   rootLifecycleServiceFactory,
-  createServiceFactory({
-    service: coreServices.rootLogger,
-    deps: {},
-    factory: () => new MockLogger(),
-  }),
   loggerServiceFactory,
 ];
 
@@ -399,7 +390,7 @@ describe('BackendInitializer', () => {
   });
 
   it('should forward errors when plugins fail to start', async () => {
-    const init = new BackendInitializer([]);
+    const init = new BackendInitializer(requiredRootFactories);
     init.add(
       createBackendPlugin({
         pluginId: 'test',
@@ -419,7 +410,7 @@ describe('BackendInitializer', () => {
   });
 
   it('should forward errors when modules fail to start', async () => {
-    const init = new BackendInitializer([]);
+    const init = new BackendInitializer(requiredRootFactories);
     init.add(testPlugin);
     init.add(
       createBackendModule({
@@ -441,7 +432,7 @@ describe('BackendInitializer', () => {
   });
 
   it('should reject duplicate plugins', async () => {
-    const init = new BackendInitializer([]);
+    const init = new BackendInitializer(requiredRootFactories);
     init.add(
       createBackendPlugin({
         pluginId: 'test',
@@ -470,7 +461,7 @@ describe('BackendInitializer', () => {
   });
 
   it('should reject duplicate modules', async () => {
-    const init = new BackendInitializer([]);
+    const init = new BackendInitializer(requiredRootFactories);
     init.add(testPlugin);
     init.add(
       createBackendModule({
@@ -505,12 +496,8 @@ describe('BackendInitializer', () => {
     const extA = createExtensionPoint<string>({ id: 'a' });
     const extB = createExtensionPoint<string>({ id: 'b' });
     const init = new BackendInitializer([
+      ...requiredRootFactories,
       rootLifecycleServiceFactory,
-      createServiceFactory({
-        service: coreServices.rootLogger,
-        deps: {},
-        factory: () => new MockLogger(),
-      }),
     ]);
     init.add(testPlugin);
     init.add(
diff --git a/packages/backend-app-api/src/wiring/BackendInitializer.ts b/packages/backend-app-api/src/wiring/BackendInitializer.ts
index b2173fb105..37b424c8ae 100644
--- a/packages/backend-app-api/src/wiring/BackendInitializer.ts
+++ b/packages/backend-app-api/src/wiring/BackendInitializer.ts
@@ -34,11 +34,11 @@ import type {
 // eslint-disable-next-line @backstage/no-relative-monorepo-imports
 import type { InternalServiceFactory } from '../../../backend-plugin-api/src/services/system/types';
 import { ForwardedError, ConflictError } from '@backstage/errors';
-import { featureDiscoveryServiceRef } from '@backstage/backend-plugin-api/alpha';
 import { DependencyGraph } from '../lib/DependencyGraph';
 import { ServiceRegistry } from './ServiceRegistry';
 import { createInitializationLogger } from './createInitializationLogger';
 import { unwrapFeature } from './helpers';
+import { featureDiscoveryLoader } from '../alpha/featureDiscoveryServiceFactory';
 
 export interface BackendRegisterInit {
   consumes: Set<ServiceOrExtensionPoint>;
@@ -150,25 +150,14 @@ export class BackendInitializer {
   }
 
   async #doStart(): Promise<void> {
+    this.add(featureDiscoveryLoader);
+
     this.#serviceRegistry.checkForCircularDeps();
 
     for (const feature of this.#registeredFeatures) {
       this.#addFeature(await feature);
     }
 
-    const featureDiscovery = await this.#serviceRegistry.get(
-      featureDiscoveryServiceRef,
-      'root',
-    );
-
-    if (featureDiscovery) {
-      const { features } = await featureDiscovery.getBackendFeatures();
-      for (const feature of features) {
-        this.#addFeature(unwrapFeature(feature));
-      }
-      this.#serviceRegistry.checkForCircularDeps();
-    }
-
     await this.#applyBackendFeatureLoaders(this.#registeredFeatureLoaders);
 
     // Initialize all root scoped services
diff --git a/packages/backend-dynamic-feature-service/api-report.md b/packages/backend-dynamic-feature-service/api-report.md
index 148825dce1..355a7efc94 100644
--- a/packages/backend-dynamic-feature-service/api-report.md
+++ b/packages/backend-dynamic-feature-service/api-report.md
@@ -112,7 +112,15 @@ export interface DynamicPluginsFactoryOptions {
   moduleLoader?(logger: LoggerService): ModuleLoader;
 }
 
-// @public (undocumented)
+// @public
+export const dynamicPluginsFeatureDiscoveryLoader: BackendFeature;
+
+// @public
+export const dynamicPluginsFeatureDiscoveryLoaderWithOptions: (
+  options?: DynamicPluginsFactoryOptions,
+) => BackendFeature;
+
+// @public @deprecated (undocumented)
 export const dynamicPluginsFeatureDiscoveryServiceFactory: ServiceFactory<
   FeatureDiscoveryService,
   'root',
@@ -154,19 +162,19 @@ export const dynamicPluginsSchemasServiceFactoryWithOptions: (
   options?: DynamicPluginsSchemasOptions,
 ) => ServiceFactory<DynamicPluginsSchemasService, 'root', 'singleton'>;
 
-// @public (undocumented)
+// @public @deprecated (undocumented)
 export const dynamicPluginsServiceFactory: ServiceFactory<
   DynamicPluginProvider,
   'root',
   'singleton'
 >;
 
-// @public (undocumented)
+// @public @deprecated (undocumented)
 export const dynamicPluginsServiceFactoryWithOptions: (
   options?: DynamicPluginsFactoryOptions,
 ) => ServiceFactory<DynamicPluginProvider, 'root', 'singleton'>;
 
-// @public (undocumented)
+// @public @deprecated (undocumented)
 export const dynamicPluginsServiceRef: ServiceRef<
   DynamicPluginProvider,
   'root',
diff --git a/packages/backend-dynamic-feature-service/src/manager/index.ts b/packages/backend-dynamic-feature-service/src/manager/index.ts
index 542bab68ac..51d9915a7c 100644
--- a/packages/backend-dynamic-feature-service/src/manager/index.ts
+++ b/packages/backend-dynamic-feature-service/src/manager/index.ts
@@ -36,6 +36,8 @@ export {
   dynamicPluginsServiceFactory,
   dynamicPluginsServiceFactoryWithOptions,
   dynamicPluginsServiceRef,
+  dynamicPluginsFeatureDiscoveryLoader,
+  dynamicPluginsFeatureDiscoveryLoaderWithOptions,
 } from './plugin-manager';
 
 export type {
diff --git a/packages/backend-dynamic-feature-service/src/manager/plugin-manager.ts b/packages/backend-dynamic-feature-service/src/manager/plugin-manager.ts
index 40746ff440..97ceb08a34 100644
--- a/packages/backend-dynamic-feature-service/src/manager/plugin-manager.ts
+++ b/packages/backend-dynamic-feature-service/src/manager/plugin-manager.ts
@@ -30,6 +30,7 @@ import {
   BackendFeature,
   LoggerService,
   coreServices,
+  createBackendFeatureLoader,
   createServiceFactory,
   createServiceRef,
 } from '@backstage/backend-plugin-api';
@@ -214,6 +215,7 @@ export class DynamicPluginManager implements DynamicPluginProvider {
 
 /**
  * @public
+ * @deprecated The `featureDiscoveryService` is deprecated in favor of using {@link dynamicPluginsFeatureDiscoveryLoader} or {@link dynamicPluginsFeatureDiscoveryLoaderWithOptions} instead.
  */
 export const dynamicPluginsServiceRef = createServiceRef<DynamicPluginProvider>(
   {
@@ -231,6 +233,7 @@ export interface DynamicPluginsFactoryOptions {
 
 /**
  * @public
+ * @deprecated Use {@link dynamicPluginsFeatureDiscoveryLoaderWithOptions} instead.
  */
 export const dynamicPluginsServiceFactoryWithOptions = (
   options?: DynamicPluginsFactoryOptions,
@@ -253,6 +256,7 @@ export const dynamicPluginsServiceFactoryWithOptions = (
 
 /**
  * @public
+ * @deprecated Use {@link dynamicPluginsFeatureDiscoveryLoader} instead.
  */
 export const dynamicPluginsServiceFactory =
   dynamicPluginsServiceFactoryWithOptions();
@@ -292,6 +296,7 @@ class DynamicPluginsEnabledFeatureDiscoveryService
 
 /**
  * @public
+ * @deprecated The `featureDiscoveryService` is deprecated in favor of using {@link dynamicPluginsFeatureDiscoveryLoader} or {@link dynamicPluginsFeatureDiscoveryLoaderWithOptions} instead.
  */
 export const dynamicPluginsFeatureDiscoveryServiceFactory =
   createServiceFactory({
@@ -305,6 +310,69 @@ export const dynamicPluginsFeatureDiscoveryServiceFactory =
     },
   });
 
+/**
+ * A function that returns a backend feature loader that uses the dynamic plugins system to discover features.
+ *
+ * @public
+ *
+ * @example
+ * Using the `dynamicPluginsFeatureDiscoveryLoaderWithOptions` loader in a backend instance:
+ * ```ts
+ * //...
+ * import { createBackend } from '@backstage/backend-defaults';
+ * import { dynamicPluginsFeatureDiscoveryLoaderWithOptions } from '@backstage/backend-dynamic-feature-service';
+ * import { myCustomModuleLoader } from './myCustomModuleLoader';
+ *
+ * const backend = createBackend();
+ * backend.add(dynamicPluginsFeatureDiscoveryLoaderWithOptions({
+ *   moduleLoader: myCustomModuleLoader
+ * }));
+ * //...
+ * backend.start();
+ * ```
+ */
+export const dynamicPluginsFeatureDiscoveryLoaderWithOptions = (
+  options?: DynamicPluginsFactoryOptions,
+) =>
+  createBackendFeatureLoader({
+    deps: {
+      config: coreServices.rootConfig,
+      logger: coreServices.rootLogger,
+    },
+    async loader({ config, logger }) {
+      const manager = await DynamicPluginManager.create({
+        config,
+        logger,
+        preferAlpha: true,
+        moduleLoader: options?.moduleLoader?.(logger),
+      });
+      const service = new DynamicPluginsEnabledFeatureDiscoveryService(manager);
+      const { features } = await service.getBackendFeatures();
+      return features;
+    },
+  });
+
+/**
+ * A backend feature loader that uses the dynamic plugins system to discover features.
+ *
+ * @public
+ *
+ * @example
+ * Using the `dynamicPluginsFeatureDiscoveryLoader` loader in a backend instance:
+ * ```ts
+ * //...
+ * import { createBackend } from '@backstage/backend-defaults';
+ * import { dynamicPluginsFeatureDiscoveryLoader } from '@backstage/backend-dynamic-feature-service';
+ *
+ * const backend = createBackend();
+ * backend.add(dynamicPluginsFeatureDiscoveryLoader);
+ * //...
+ * backend.start();
+ * ```
+ */
+export const dynamicPluginsFeatureDiscoveryLoader =
+  dynamicPluginsFeatureDiscoveryLoaderWithOptions();
+
 function isBackendFeature(value: unknown): value is BackendFeature {
   return (
     !!value &&
diff --git a/packages/backend-plugin-api/api-report-alpha.md b/packages/backend-plugin-api/api-report-alpha.md
index 0f4348336a..dea357502e 100644
--- a/packages/backend-plugin-api/api-report-alpha.md
+++ b/packages/backend-plugin-api/api-report-alpha.md
@@ -14,7 +14,7 @@ export interface FeatureDiscoveryService {
   }>;
 }
 
-// @alpha
+// @alpha @deprecated
 export const featureDiscoveryServiceRef: ServiceRef<
   FeatureDiscoveryService,
   'root',
diff --git a/packages/backend-plugin-api/src/alpha.ts b/packages/backend-plugin-api/src/alpha.ts
index baee739f49..e57bd19de1 100644
--- a/packages/backend-plugin-api/src/alpha.ts
+++ b/packages/backend-plugin-api/src/alpha.ts
@@ -27,6 +27,7 @@ export interface FeatureDiscoveryService {
 /**
  * An optional service that can be used to dynamically load in additional BackendFeatures at runtime.
  * @alpha
+ * @deprecated The `featureDiscoveryServiceRef` is deprecated in favor of using {@link @backstage/backend-app-api#featureDiscoveryLoader} instead.
  */
 export const featureDiscoveryServiceRef =
   createServiceRef<FeatureDiscoveryService>({