diff --git a/packages/frontend-app-api/src/tree/instantiateAppNodeTree.test.ts b/packages/frontend-app-api/src/tree/instantiateAppNodeTree.test.ts
index f24a9e17f3..a000e016be 100644
--- a/packages/frontend-app-api/src/tree/instantiateAppNodeTree.test.ts
+++ b/packages/frontend-app-api/src/tree/instantiateAppNodeTree.test.ts
@@ -925,6 +925,24 @@ describe('instantiateAppNodeTree', () => {
         });
       });
 
+      it('should create an extension passed through an extension factory middleware', () => {
+        const attachments = new Map();
+        const instance = createAppNodeInstance({
+          node: makeNode(simpleExtension),
+          attachments,
+          apis: testApis,
+          *extensionFactoryMiddleware(originalFactory) {
+            const output = originalFactory({
+              config: { output: 'modified' },
+            });
+            yield* output;
+          },
+        });
+
+        expect(Array.from(instance.getDataRefs())).toEqual([testDataRef]);
+        expect(instance.getData(testDataRef)).toEqual('modified');
+      });
+
       it('should refuse to create an extension with invalid config', () => {
         expect(() =>
           createAppNodeInstance({
diff --git a/packages/frontend-app-api/src/wiring/createSpecializedApp.test.tsx b/packages/frontend-app-api/src/wiring/createSpecializedApp.test.tsx
index a1399d786a..e269961d52 100644
--- a/packages/frontend-app-api/src/wiring/createSpecializedApp.test.tsx
+++ b/packages/frontend-app-api/src/wiring/createSpecializedApp.test.tsx
@@ -29,7 +29,7 @@ import {
 } from '@backstage/frontend-plugin-api';
 import { screen, render } from '@testing-library/react';
 import { createSpecializedApp } from './createSpecializedApp';
-import { mockApis } from '@backstage/test-utils';
+import { mockApis, TestApiRegistry } from '@backstage/test-utils';
 import React from 'react';
 import {
   configApiRef,
@@ -37,7 +37,7 @@ import {
   featureFlagsApiRef,
 } from '@backstage/core-plugin-api';
 import { MemoryRouter } from 'react-router-dom';
-import { ApiProvider } from '@backstage/core-app-api';
+import { ApiProvider, ConfigReader } from '@backstage/core-app-api';
 
 describe('createSpecializedApp', () => {
   it('should render the root app', () => {
@@ -166,6 +166,81 @@ describe('createSpecializedApp', () => {
     render(app.createRoot());
 
     expect(screen.getByText('flags:test=a,test=b')).toBeInTheDocument();
+
+    expect(app.apis).toMatchInlineSnapshot(`
+      ApiResolver {
+        "apis": Map {
+          "core.featureflags" => {
+            "getRegisteredFlags": [Function],
+            "registerFlag": [Function],
+          },
+        },
+        "factories": ApiFactoryRegistry {
+          "factories": Map {
+            "core.featureflags" => {
+              "factory": {
+                "api": ApiRefImpl {
+                  "config": {
+                    "id": "core.featureflags",
+                  },
+                },
+                "deps": {},
+                "factory": [Function],
+              },
+              "priority": 10,
+            },
+            "core.app-tree" => {
+              "factory": {
+                "api": ApiRefImpl {
+                  "config": {
+                    "id": "core.app-tree",
+                  },
+                },
+                "deps": {},
+                "factory": [Function],
+              },
+              "priority": 100,
+            },
+            "core.config" => {
+              "factory": {
+                "api": ApiRefImpl {
+                  "config": {
+                    "id": "core.config",
+                  },
+                },
+                "deps": {},
+                "factory": [Function],
+              },
+              "priority": 100,
+            },
+            "core.route-resolution" => {
+              "factory": {
+                "api": ApiRefImpl {
+                  "config": {
+                    "id": "core.route-resolution",
+                  },
+                },
+                "deps": {},
+                "factory": [Function],
+              },
+              "priority": 100,
+            },
+            "core.identity" => {
+              "factory": {
+                "api": ApiRefImpl {
+                  "config": {
+                    "id": "core.identity",
+                  },
+                },
+                "deps": {},
+                "factory": [Function],
+              },
+              "priority": 100,
+            },
+          },
+        },
+      }
+    `);
   });
 
   it('should intitialize the APIs in the correct order to allow for overrides', () => {
@@ -237,10 +312,59 @@ describe('createSpecializedApp', () => {
     expect(mockAnalyticsApi).toHaveBeenCalled();
   });
 
+  it('should use provided apis', async () => {
+    const app = createSpecializedApp({
+      apis: TestApiRegistry.from([
+        configApiRef,
+        new ConfigReader({ anything: 'config' }),
+      ]),
+      features: [
+        createFrontendPlugin({
+          id: 'test',
+          extensions: [
+            createExtension({
+              attachTo: { id: 'root', input: 'app' },
+              output: [coreExtensionData.reactElement],
+              factory: ({ apis }) => [
+                coreExtensionData.reactElement(
+                  <div>
+                    providedApis:
+                    {apis.get(configApiRef)!.getString('anything')}
+                  </div>,
+                ),
+              ],
+            }),
+          ],
+        }),
+      ],
+    });
+
+    render(app.createRoot());
+
+    expect(screen.getByText('providedApis:config')).toBeInTheDocument();
+
+    expect(app.apis).toMatchInlineSnapshot(`
+      TestApiRegistry {
+        "apis": Map {
+          "core.config" => ConfigReader {
+            "context": "mock-config",
+            "data": {
+              "anything": "config",
+            },
+            "fallback": undefined,
+            "filteredKeys": undefined,
+            "notifiedFilteredKeys": Set {},
+            "prefix": "",
+          },
+        },
+      }
+    `);
+  });
+
   it('should make the app structure available through the AppTreeApi', async () => {
     let appTreeApi: AppTreeApi | undefined = undefined;
 
-    createSpecializedApp({
+    const { tree } = createSpecializedApp({
       features: [
         createFrontendPlugin({
           id: 'test',
@@ -265,6 +389,55 @@ describe('createSpecializedApp', () => {
         ]
       </root>"
     `);
+
+    expect(tree).toMatchInlineSnapshot(`
+      {
+        "nodes": Map {
+          "test" => {
+            "attachments": undefined,
+            "id": "test",
+            "output": [
+              "core.reactElement",
+            ],
+          },
+          "root" => {
+            "attachments": {
+              "app": [
+                {
+                  "attachments": undefined,
+                  "id": "test",
+                  "output": [
+                    "core.reactElement",
+                  ],
+                },
+              ],
+            },
+            "id": "root",
+            "output": [
+              "core.reactElement",
+            ],
+          },
+        },
+        "orphans": [],
+        "root": {
+          "attachments": {
+            "app": [
+              {
+                "attachments": undefined,
+                "id": "test",
+                "output": [
+                  "core.reactElement",
+                ],
+              },
+            ],
+          },
+          "id": "root",
+          "output": [
+            "core.reactElement",
+          ],
+        },
+      }
+    `);
   });
 
   it('should support route bindings', async () => {
diff --git a/packages/frontend-defaults/src/createApp.test.tsx b/packages/frontend-defaults/src/createApp.test.tsx
index 899d5d1640..c11bb138e0 100644
--- a/packages/frontend-defaults/src/createApp.test.tsx
+++ b/packages/frontend-defaults/src/createApp.test.tsx
@@ -395,6 +395,46 @@ describe('createApp', () => {
     expect(screen.queryByText('Custom app root element')).toBeNull();
   });
 
+  it('should use a custom extensionFactoryMiddleware', async () => {
+    const app = createApp({
+      configLoader: async () => ({ config: mockApis.config() }),
+      features: [
+        appPlugin,
+        createFrontendPlugin({
+          id: 'test-plugin',
+          extensions: [
+            PageBlueprint.make({
+              name: 'test-page',
+              params: {
+                defaultPath: '/',
+                loader: async () => <>Test Page</>,
+              },
+            }),
+          ],
+        }),
+      ],
+      *extensionFactoryMiddleware(originalFactory, context) {
+        const output = originalFactory();
+        yield* output;
+        const element = output.get(coreExtensionData.reactElement);
+
+        if (element) {
+          yield coreExtensionData.reactElement(
+            <div data-testid={`wrapped(${context.node.spec.id})`}>
+              {element}
+            </div>,
+          );
+        }
+      },
+    });
+
+    await renderWithEffects(app.createRoot());
+
+    await expect(
+      screen.findByTestId('wrapped(page:test-plugin/test-page)'),
+    ).resolves.toHaveTextContent('Test Page');
+  });
+
   describe('modules', () => {
     it('should be able to override extensions with a plugin extension override', async () => {
       const mod = createFrontendModule({