diff --git a/.changeset/wet-rivers-travel.md b/.changeset/wet-rivers-travel.md
new file mode 100644
index 0000000000..44dedf3ccb
--- /dev/null
+++ b/.changeset/wet-rivers-travel.md
@@ -0,0 +1,5 @@
+---
+'@backstage/backend-defaults': patch
+---
+
+The `RootConfigFactoryOptions` have been deprecated alongside the deprecation of service factory options. For more information on how to customize the config service, see the [Root Config Service docs](https://backstage.io/docs/backend-system/core-services/root-config#configuring-the-service).
diff --git a/docs/backend-system/core-services/root-config.md b/docs/backend-system/core-services/root-config.md
index 7cdc10f38c..9561a8f0cd 100644
--- a/docs/backend-system/core-services/root-config.md
+++ b/docs/backend-system/core-services/root-config.md
@@ -36,12 +36,12 @@ createBackendPlugin({
 
 ## Configuring the service
 
-There's additional configuration that you can optionally pass to setup the `config` core service.
+There are several APIs from the `@backstage/config-loader` package that allow you to customize the implementation of the config service. The default implementation uses the `ConfigSources.default` method, which has several options, for example:
 
 - `argv` - Override the arguments that are passed to the config loader, instead of using `process.argv`
 - `remote` - Configure remote configuration loading
 
-You can configure these additional options by adding an override for the core service when calling `createBackend` like follows:
+You can use these to create your own config service implementation:
 
 ```ts
 import { rootConfigServiceFactory } from '@backstage/backend-app-api';
@@ -49,14 +49,24 @@ import { rootConfigServiceFactory } from '@backstage/backend-app-api';
 const backend = createBackend();
 
 backend.add(
-  rootConfigServiceFactory({
-    argv: [
-      '--config',
-      '/backstage/app-config.development.yaml',
-      '--config',
-      '/backstage/app-config.yaml',
-    ],
-    remote: { reloadIntervalSeconds: 60 },
+  createServiceFactory({
+    service: coreServices.rootConfig,
+    deps: {},
+    async factory() {
+      const source = ConfigSources.default({
+        argv: [
+          '--config',
+          '/backstage/app-config.development.yaml',
+          '--config',
+          '/backstage/app-config.yaml',
+        ],
+        remote: { reloadIntervalSeconds: 60 },
+      });
+      console.log(`Loading config from ${source}`);
+      return await ConfigSources.toConfig(source);
+    },
   }),
 );
 ```
+
+You can also use other config source such as `StaticConfigSource` and combine them with other sources using `ConfigSources.merge(...)`. You can also create your own config source by implementing the `ConfigSource` interface.
diff --git a/packages/backend-defaults/api-report-rootConfig.md b/packages/backend-defaults/api-report-rootConfig.md
index 24e827f520..8ad2e01a90 100644
--- a/packages/backend-defaults/api-report-rootConfig.md
+++ b/packages/backend-defaults/api-report-rootConfig.md
@@ -17,7 +17,7 @@ export function createConfigSecretEnumerator(options: {
   schema?: ConfigSchema;
 }): Promise<(config: Config) => Iterable<string>>;
 
-// @public
+// @public @deprecated
 export interface RootConfigFactoryOptions {
   argv?: string[];
   remote?: Pick<RemoteConfigSourceOptions, 'reloadInterval'>;
diff --git a/packages/backend-defaults/src/entrypoints/rootConfig/rootConfigServiceFactory.ts b/packages/backend-defaults/src/entrypoints/rootConfig/rootConfigServiceFactory.ts
index 5752a9c634..7bcb9ef56b 100644
--- a/packages/backend-defaults/src/entrypoints/rootConfig/rootConfigServiceFactory.ts
+++ b/packages/backend-defaults/src/entrypoints/rootConfig/rootConfigServiceFactory.ts
@@ -31,6 +31,7 @@ import {
  * for more information.
  *
  * @public
+ * @deprecated These service options will be removed, please use the `ConfigSources` API from `@backstage/config-loader` to implement your own version of the service factory instead.
  */
 export interface RootConfigFactoryOptions {
   /**