diff --git a/.changeset/breezy-cobras-sin.md b/.changeset/breezy-cobras-sin.md
new file mode 100644
index 0000000000..93b296c455
--- /dev/null
+++ b/.changeset/breezy-cobras-sin.md
@@ -0,0 +1,5 @@
+---
+'@backstage/frontend-app-api': minor
+---
+
+**BREAKING**: Removed the experimental `createExtensionTree` API.
diff --git a/packages/app/src/App.tsx b/packages/app/src/App.tsx
index d2dde95f68..90190b50be 100644
--- a/packages/app/src/App.tsx
+++ b/packages/app/src/App.tsx
@@ -27,12 +27,7 @@ import {
   RELATION_PROVIDES_API,
 } from '@backstage/catalog-model';
 import { createApp } from '@backstage/app-defaults';
-import {
-  AppRouter,
-  ConfigReader,
-  defaultConfigLoader,
-  FlatRoutes,
-} from '@backstage/core-app-api';
+import { AppRouter, FlatRoutes } from '@backstage/core-app-api';
 import {
   AlertDisplay,
   OAuthRequestDialog,
@@ -112,10 +107,6 @@ import { PuppetDbPage } from '@backstage/plugin-puppetdb';
 import { DevToolsPage } from '@backstage/plugin-devtools';
 import { customDevToolsPage } from './components/devtools/CustomDevToolsPage';
 import { CatalogUnprocessedEntitiesPage } from '@backstage/plugin-catalog-unprocessed-entities';
-import {
-  createExtensionTree,
-  ExtensionTree,
-} from '@backstage/frontend-app-api';
 
 const app = createApp({
   apis,
@@ -162,14 +153,6 @@ const app = createApp({
   },
 });
 
-/* HIGHLY EXPERIMENTAL. DO NOT USE THIS IN YOUR APP */
-let extensionTree: ExtensionTree | undefined;
-if (process.env.NODE_ENV !== 'test') {
-  extensionTree = createExtensionTree({
-    config: ConfigReader.fromConfigs(await defaultConfigLoader()),
-  });
-}
-
 const routes = (
   <FlatRoutes>
     <Route path="/" element={<Navigate to="catalog" />} />
@@ -258,10 +241,6 @@ const routes = (
       path="/tech-radar"
       element={<TechRadarPage width={1500} height={800} />}
     />
-    {
-      /* HIGHLY EXPERIMENTAL. DO NOT USE THIS IN YOUR APP */ extensionTree?.getRootRoutes() ??
-        null
-    }
     <Route path="/lighthouse" element={<LighthousePage />} />
     <Route path="/api-docs" element={<ApiExplorerPage />} />
     <Route path="/gcp-projects" element={<GcpProjectsPage />} />
@@ -302,7 +281,7 @@ export default app.createRoot(
     <OAuthRequestDialog />
     <AppRouter>
       <VisitListener />
-      <Root extensionTree={extensionTree}>{routes}</Root>
+      <Root>{routes}</Root>
     </AppRouter>
   </>,
 );
diff --git a/packages/app/src/components/Root/Root.tsx b/packages/app/src/components/Root/Root.tsx
index 066ba4d05b..ec5f9dabe2 100644
--- a/packages/app/src/components/Root/Root.tsx
+++ b/packages/app/src/components/Root/Root.tsx
@@ -84,7 +84,6 @@ const SidebarLogo = () => {
 
 export const Root = ({
   children,
-  extensionTree,
 }: PropsWithChildren<{ extensionTree?: ExtensionTree }>) => (
   <SidebarPage>
     <Sidebar>
@@ -166,10 +165,6 @@ export const Root = ({
             to="cost-insights"
             text="Cost Insights"
           />
-          {
-            /* HIGHLY EXPERIMENTAL. DO NOT USE THIS IN YOUR APP */ extensionTree?.getSidebarItems() ??
-              null
-          }
           <SidebarItem icon={Score} to="score-board" text="Score board" />
         </SidebarScrollWrapper>
         <SidebarDivider />
diff --git a/packages/frontend-app-api/api-report.md b/packages/frontend-app-api/api-report.md
index d0aadb7e8c..3236b05a01 100644
--- a/packages/frontend-app-api/api-report.md
+++ b/packages/frontend-app-api/api-report.md
@@ -3,9 +3,7 @@
 > Do not edit this file. It is a report generated by [API Extractor](https://api-extractor.com/).
 
 ```ts
-import { Config } from '@backstage/config';
 import { ConfigApi } from '@backstage/core-plugin-api';
-import { ExtensionDataRef } from '@backstage/frontend-plugin-api';
 import { ExternalRouteRef } from '@backstage/frontend-plugin-api';
 import { FrontendFeature } from '@backstage/frontend-plugin-api';
 import { IconComponent } from '@backstage/core-plugin-api';
@@ -48,9 +46,6 @@ export type CreateAppRouteBinder = <
   >,
 ) => void;
 
-// @public (undocumented)
-export function createExtensionTree(options: { config: Config }): ExtensionTree;
-
 // @public
 export function createSpecializedApp(options?: {
   icons?: {
@@ -62,24 +57,4 @@ export function createSpecializedApp(options?: {
 }): {
   createRoot(): JSX_2.Element;
 };
-
-// @public (undocumented)
-export interface ExtensionTree {
-  // (undocumented)
-  getExtension(id: string): ExtensionTreeNode | undefined;
-  // (undocumented)
-  getExtensionAttachments(id: string, inputName: string): ExtensionTreeNode[];
-  // (undocumented)
-  getRootRoutes(): JSX_2.Element[];
-  // (undocumented)
-  getSidebarItems(): JSX_2.Element[];
-}
-
-// @public (undocumented)
-export interface ExtensionTreeNode {
-  // (undocumented)
-  getData<T>(ref: ExtensionDataRef<T>): T | undefined;
-  // (undocumented)
-  id: string;
-}
 ```
diff --git a/packages/frontend-app-api/src/wiring/createApp.tsx b/packages/frontend-app-api/src/wiring/createApp.tsx
index 6966ef87c3..635e36aace 100644
--- a/packages/frontend-app-api/src/wiring/createApp.tsx
+++ b/packages/frontend-app-api/src/wiring/createApp.tsx
@@ -15,7 +15,7 @@
  */
 
 import React, { JSX } from 'react';
-import { ConfigReader, Config } from '@backstage/config';
+import { ConfigReader } from '@backstage/config';
 import {
   AppTree,
   appTreeApiRef,
@@ -24,16 +24,12 @@ import {
   coreExtensionData,
   createApiExtension,
   createComponentExtension,
-  createNavItemExtension,
   createThemeExtension,
   createTranslationExtension,
-  ExtensionDataRef,
   FrontendFeature,
   iconsApiRef,
-  RouteRef,
   RouteResolutionApi,
   routeResolutionApiRef,
-  useRouteRef,
 } from '@backstage/frontend-plugin-api';
 import { App } from '../extensions/App';
 import { AppRoutes } from '../extensions/AppRoutes';
@@ -47,7 +43,6 @@ import {
   configApiRef,
   IconComponent,
   featureFlagsApiRef,
-  attachComponentData,
   identityApiRef,
   AppTheme,
 } from '@backstage/core-plugin-api';
@@ -78,8 +73,6 @@ import { I18nextTranslationApi } from '../../../core-app-api/src/apis/implementa
 import { resolveExtensionDefinition } from '../../../frontend-plugin-api/src/wiring/resolveExtensionDefinition';
 // eslint-disable-next-line @backstage/no-relative-monorepo-imports
 import { apis as defaultApis } from '../../../app-defaults/src/defaults';
-import { Route } from 'react-router-dom';
-import { SidebarItem } from '@backstage/core-components';
 import { DarkTheme, LightTheme } from '../extensions/themes';
 import {
   oauthRequestDialogAppRootElement,
@@ -100,7 +93,6 @@ import {
   DefaultErrorBoundaryComponent,
   DefaultNotFoundErrorPageComponent,
 } from '../extensions/components';
-import { AppNode } from '@backstage/frontend-plugin-api';
 import { InternalAppContext } from './InternalAppContext';
 import { AppRoot } from '../extensions/AppRoot';
 // eslint-disable-next-line @backstage/no-relative-monorepo-imports
@@ -132,106 +124,6 @@ export const builtinExtensions = [
   ...DefaultApis,
 ].map(def => resolveExtensionDefinition(def));
 
-/** @public */
-export interface ExtensionTreeNode {
-  id: string;
-  getData<T>(ref: ExtensionDataRef<T>): T | undefined;
-}
-
-/** @public */
-export interface ExtensionTree {
-  getExtension(id: string): ExtensionTreeNode | undefined;
-  getExtensionAttachments(id: string, inputName: string): ExtensionTreeNode[];
-  getRootRoutes(): JSX.Element[];
-  getSidebarItems(): JSX.Element[];
-}
-
-/** @public */
-export function createExtensionTree(options: {
-  config: Config;
-}): ExtensionTree {
-  const features = getAvailableFeatures(options.config);
-  const tree = createAppTree({
-    features,
-    builtinExtensions,
-    config: options.config,
-  });
-
-  function convertNode(node?: AppNode): ExtensionTreeNode | undefined {
-    return (
-      node && {
-        id: node.spec.id,
-        getData<T>(ref: ExtensionDataRef<T>): T | undefined {
-          return node.instance?.getData(ref);
-        },
-      }
-    );
-  }
-
-  return {
-    getExtension(id: string): ExtensionTreeNode | undefined {
-      return convertNode(tree.nodes.get(id));
-    },
-    getExtensionAttachments(
-      id: string,
-      inputName: string,
-    ): ExtensionTreeNode[] {
-      return (
-        tree.nodes
-          .get(id)
-          ?.edges.attachments.get(inputName)
-          ?.map(convertNode)
-          .filter((node): node is ExtensionTreeNode => Boolean(node)) ?? []
-      );
-    },
-    getRootRoutes(): JSX.Element[] {
-      return this.getExtensionAttachments('app/routes', 'routes').map(node => {
-        const path = node.getData(coreExtensionData.routePath);
-        const element = node.getData(coreExtensionData.reactElement);
-        const routeRef = node.getData(coreExtensionData.routeRef);
-        if (!path || !element) {
-          throw new Error(`Invalid route extension: ${node.id}`);
-        }
-        const Component = () => {
-          return element;
-        };
-        attachComponentData(Component, 'core.mountPoint', routeRef);
-
-        return <Route path={path} element={<Component />} />;
-      });
-    },
-    getSidebarItems(): JSX.Element[] {
-      const RoutedSidebarItem = (props: {
-        title: string;
-        routeRef: RouteRef;
-        icon: IconComponent;
-      }): React.JSX.Element => {
-        const location = useRouteRef(props.routeRef);
-        return (
-          <SidebarItem icon={props.icon} to={location()} text={props.title} />
-        );
-      };
-
-      return this.getExtensionAttachments('app/nav', 'items')
-        .map((node, index) => {
-          const target = node.getData(createNavItemExtension.targetDataRef);
-          if (!target) {
-            return null;
-          }
-          return (
-            <RoutedSidebarItem
-              key={index}
-              title={target.title}
-              icon={target.icon}
-              routeRef={target.routeRef}
-            />
-          );
-        })
-        .filter((x): x is JSX.Element => !!x);
-    },
-  };
-}
-
 function deduplicateFeatures(
   allFeatures: FrontendFeature[],
 ): FrontendFeature[] {
diff --git a/packages/frontend-app-api/src/wiring/index.ts b/packages/frontend-app-api/src/wiring/index.ts
index 00c6458bd5..d1498514c8 100644
--- a/packages/frontend-app-api/src/wiring/index.ts
+++ b/packages/frontend-app-api/src/wiring/index.ts
@@ -17,8 +17,5 @@
 export {
   createApp,
   createSpecializedApp,
-  createExtensionTree,
   type CreateAppFeatureLoader,
-  type ExtensionTreeNode,
-  type ExtensionTree,
 } from './createApp';