diff --git a/ui/desktop/src/components/ConfigContext.tsx b/ui/desktop/src/components/ConfigContext.tsx
index f676deb1..434cad8c 100644
--- a/ui/desktop/src/components/ConfigContext.tsx
+++ b/ui/desktop/src/components/ConfigContext.tsx
@@ -9,7 +9,7 @@ import {
   removeExtension as apiRemoveExtension,
   providers,
 } from '../api';
-import { syncBundledExtensions } from './settings/extensions';
+import { pruneDeprecatedBundledExtensions, syncBundledExtensions } from './settings/extensions';
 import type {
   ConfigResponse,
   UpsertConfigQuery,
@@ -88,16 +88,19 @@ export const ConfigProvider: React.FC<ConfigProviderProps> = ({ children }) => {
     [reloadConfig]
   );
 
-  const read = useCallback(async (key: string, is_secret: boolean = false, options?: { throwOnError?: boolean }) => {
-    const query: ConfigKeyQuery = { key: key, is_secret: is_secret };
-    const response = await readConfig({
-      body: query,
-    });
-    if (options?.throwOnError && response.error) {
-      throw response.error;
-    }
-    return response.data;
-  }, []);
+  const read = useCallback(
+    async (key: string, is_secret: boolean = false, options?: { throwOnError?: boolean }) => {
+      const query: ConfigKeyQuery = { key: key, is_secret: is_secret };
+      const response = await readConfig({
+        body: query,
+      });
+      if (options?.throwOnError && response.error) {
+        throw response.error;
+      }
+      return response.data;
+    },
+    []
+  );
 
   const remove = useCallback(
     async (key: string, is_secret: boolean) => {
@@ -226,6 +229,10 @@ export const ConfigProvider: React.FC<ConfigProviderProps> = ({ children }) => {
           const query: ExtensionQuery = { name, config, enabled };
           await apiAddExtension({ body: query });
         };
+        const removeExtensionForSync = async (name: string) => {
+          await apiRemoveExtension({ path: { name } });
+        };
+        extensions = await pruneDeprecatedBundledExtensions(extensions, removeExtensionForSync);
         await syncBundledExtensions(extensions, addExtensionForSync);
         // Reload extensions after sync
         const refreshedResponse = await apiGetExtensions();
diff --git a/ui/desktop/src/components/bottom_menu/BottomMenuExtensionSelection.tsx b/ui/desktop/src/components/bottom_menu/BottomMenuExtensionSelection.tsx
index e7b2758c..2128b134 100644
--- a/ui/desktop/src/components/bottom_menu/BottomMenuExtensionSelection.tsx
+++ b/ui/desktop/src/components/bottom_menu/BottomMenuExtensionSelection.tsx
@@ -7,6 +7,7 @@ import { Switch } from '../ui/switch';
 import { FixedExtensionEntry, useConfig } from '../ConfigContext';
 import { toastService } from '../../toasts';
 import { formatExtensionName } from '../settings/extensions/subcomponents/ExtensionList';
+import { nameToKey } from '../settings/extensions/utils';
 import { ExtensionConfig, getSessionExtensions } from '../../api';
 import { addToAgent, removeFromAgent } from '../settings/extensions/agent-api';
 import {
@@ -230,15 +231,29 @@ export const BottomMenuExtensionSelection = ({ sessionId }: BottomMenuExtensionS
       );
     }
 
-    const sessionExtensionNames = new Set(sessionExtensions.map((ext) => ext.name));
+    const sessionExtensionKeys = new Set(sessionExtensions.map((ext) => nameToKey(ext.name)));
+    const globalExtensionKeys = new Set(allExtensions.map((ext) => nameToKey(ext.name)));
 
-    return allExtensions.map(
+    const mergedExtensions = allExtensions.map(
       (ext) =>
         ({
           ...ext,
-          enabled: sessionExtensionNames.has(ext.name),
+          enabled: sessionExtensionKeys.has(nameToKey(ext.name)),
         }) as FixedExtensionEntry
     );
+
+    for (const sessionExtension of sessionExtensions) {
+      if (globalExtensionKeys.has(nameToKey(sessionExtension.name))) {
+        continue;
+      }
+
+      mergedExtensions.push({
+        ...sessionExtension,
+        enabled: true,
+      });
+    }
+
+    return mergedExtensions;
     // eslint-disable-next-line react-hooks/exhaustive-deps
   }, [allExtensions, sessionExtensions, isHubView, hubUpdateTrigger]);
 
@@ -266,6 +281,9 @@ export const BottomMenuExtensionSelection = ({ sessionId }: BottomMenuExtensionS
     return extensionsList.filter((ext) => ext.enabled).length;
   }, [extensionsList]);
 
+  const shouldHideTrigger =
+    extensionsList.length === 0 || (!isHubView && !isSessionExtensionsLoaded);
+
   return (
     <DropdownMenu
       open={isOpen}
@@ -284,7 +302,7 @@ export const BottomMenuExtensionSelection = ({ sessionId }: BottomMenuExtensionS
     >
       <DropdownMenuTrigger asChild>
         <button
-          className={`flex items-center [&_svg]:size-4 text-text-primary/70 hover:text-text-primary hover:scale-100 hover:bg-transparent text-xs cursor-pointer ${allExtensions.length === 0 || (!isHubView && !isSessionExtensionsLoaded) ? 'invisible' : ''}`}
+          className={`flex items-center [&_svg]:size-4 text-text-primary/70 hover:text-text-primary hover:scale-100 hover:bg-transparent text-xs cursor-pointer ${shouldHideTrigger ? 'invisible' : ''}`}
           title={intl.formatMessage(i18n.manageExtensions)}
         >
           <Puzzle className="mr-1 h-4 w-4" />
@@ -309,7 +327,9 @@ export const BottomMenuExtensionSelection = ({ sessionId }: BottomMenuExtensionS
             autoFocus
           />
           <p className="text-xs text-text-primary/60 mt-1.5">
-            {intl.formatMessage(isHubView ? i18n.extensionsForNewChats : i18n.extensionsForThisSession)}
+            {intl.formatMessage(
+              isHubView ? i18n.extensionsForNewChats : i18n.extensionsForThisSession
+            )}
           </p>
         </div>
         <div
@@ -319,7 +339,9 @@ export const BottomMenuExtensionSelection = ({ sessionId }: BottomMenuExtensionS
         >
           {sortedExtensions.length === 0 ? (
             <div className="px-2 py-4 text-center text-sm text-text-primary/70">
-              {intl.formatMessage(searchQuery ? i18n.noExtensionsFound : i18n.noExtensionsAvailable)}
+              {intl.formatMessage(
+                searchQuery ? i18n.noExtensionsFound : i18n.noExtensionsAvailable
+              )}
             </div>
           ) : (
             sortedExtensions.map((ext) => {
diff --git a/ui/desktop/src/components/settings/extensions/bundled-extensions.test.ts b/ui/desktop/src/components/settings/extensions/bundled-extensions.test.ts
index 50e63ef1..cc23ea01 100644
--- a/ui/desktop/src/components/settings/extensions/bundled-extensions.test.ts
+++ b/ui/desktop/src/components/settings/extensions/bundled-extensions.test.ts
@@ -1,5 +1,5 @@
 import { describe, it, expect, vi } from 'vitest';
-import { isDeprecatedGoogleDriveExtension, syncBundledExtensions } from './bundled-extensions';
+import { pruneDeprecatedBundledExtensions, syncBundledExtensions } from './bundled-extensions';
 import type { FixedExtensionEntry } from '../../ConfigContext';
 
 vi.mock('./bundled-extensions.json', () => ({
@@ -28,143 +28,11 @@ vi.mock('./bundled-extensions.json', () => ({
   ],
 }));
 
-describe('isDeprecatedGoogleDriveExtension', () => {
-  it('returns true for builtin googledrive', () => {
-    const ext = {
-      name: 'Google Drive',
-      type: 'builtin',
-      description: 'Google Drive extension',
-      enabled: true,
-      bundled: true,
-    } as FixedExtensionEntry;
-    expect(isDeprecatedGoogleDriveExtension(ext)).toBe(true);
-  });
-
-  it('returns true for builtin google_drive', () => {
-    const ext = {
-      name: 'google_drive',
-      type: 'builtin',
-      description: 'Google Drive extension',
-      enabled: true,
-      bundled: true,
-    } as FixedExtensionEntry;
-    expect(isDeprecatedGoogleDriveExtension(ext)).toBe(true);
-  });
-
-  it('returns true for stdio googledrive with GOOGLE_DRIVE_CREDENTIALS_PATH', () => {
-    const ext = {
-      name: 'Google Drive',
-      type: 'stdio',
-      description: 'Google Drive extension',
-      cmd: 'some-cmd',
-      args: [],
-      env_keys: ['GOOGLE_DRIVE_CREDENTIALS_PATH'],
-      enabled: true,
-      bundled: true,
-    } as FixedExtensionEntry;
-    expect(isDeprecatedGoogleDriveExtension(ext)).toBe(true);
-  });
-
-  it('returns true for stdio googledrive with GOOGLE_DRIVE_OAUTH_PATH', () => {
-    const ext = {
-      name: 'Google Drive',
-      type: 'stdio',
-      description: 'Google Drive extension',
-      cmd: 'some-cmd',
-      args: [],
-      env_keys: ['GOOGLE_DRIVE_OAUTH_PATH'],
-      enabled: true,
-      bundled: true,
-    } as FixedExtensionEntry;
-    expect(isDeprecatedGoogleDriveExtension(ext)).toBe(true);
-  });
-
-  it('returns false for stdio googledrive without deprecated env keys', () => {
-    const ext = {
-      name: 'Google Drive',
-      type: 'stdio',
-      description: 'Google Drive extension',
-      cmd: 'some-cmd',
-      args: [],
-      env_keys: [],
-      enabled: true,
-      bundled: true,
-    } as FixedExtensionEntry;
-    expect(isDeprecatedGoogleDriveExtension(ext)).toBe(false);
-  });
-
-  it('returns false for non-googledrive extensions', () => {
-    const ext = {
-      name: 'developer',
-      type: 'builtin',
-      description: 'Developer tools',
-      enabled: true,
-      bundled: true,
-    } as FixedExtensionEntry;
-    expect(isDeprecatedGoogleDriveExtension(ext)).toBe(false);
-  });
-
-  it('returns false for non-googledrive stdio with those env keys', () => {
-    const ext = {
-      name: 'some-other-ext',
-      type: 'stdio',
-      description: 'Other extension',
-      cmd: 'some-cmd',
-      args: [],
-      env_keys: ['GOOGLE_DRIVE_CREDENTIALS_PATH'],
-      enabled: true,
-      bundled: true,
-    } as FixedExtensionEntry;
-    expect(isDeprecatedGoogleDriveExtension(ext)).toBe(false);
-  });
-});
+vi.mock('./deprecated-bundled-extensions.json', () => ({
+  default: [{ id: 'googledrive' }, { id: 'old-bundled-extension' }],
+}));
 
 describe('syncBundledExtensions', () => {
-  it('overwrites deprecated builtin googledrive extension', async () => {
-    const addExtensionFn = vi.fn().mockResolvedValue(undefined);
-    const existingExtensions = [
-      {
-        name: 'googledrive',
-        type: 'builtin',
-        description: 'Google Drive',
-        enabled: true,
-        bundled: true,
-      },
-    ] as FixedExtensionEntry[];
-
-    await syncBundledExtensions(existingExtensions, addExtensionFn);
-
-    expect(addExtensionFn).toHaveBeenCalledWith(
-      'googledrive',
-      expect.objectContaining({ type: 'stdio', bundled: true }),
-      true
-    );
-  });
-
-  it('overwrites stdio googledrive with deprecated env keys', async () => {
-    const addExtensionFn = vi.fn().mockResolvedValue(undefined);
-    const existingExtensions = [
-      {
-        name: 'googledrive',
-        type: 'stdio',
-        description: 'Google Drive',
-        cmd: 'some-cmd',
-        args: [],
-        env_keys: ['GOOGLE_DRIVE_CREDENTIALS_PATH'],
-        enabled: true,
-        bundled: true,
-      },
-    ] as FixedExtensionEntry[];
-
-    await syncBundledExtensions(existingExtensions, addExtensionFn);
-
-    expect(addExtensionFn).toHaveBeenCalledWith(
-      'googledrive',
-      expect.objectContaining({ type: 'stdio', bundled: true, env_keys: [] }),
-      true
-    );
-  });
-
   it('skips already bundled non-deprecated extensions', async () => {
     const addExtensionFn = vi.fn().mockResolvedValue(undefined);
     const existingExtensions = [
@@ -187,3 +55,82 @@ describe('syncBundledExtensions', () => {
     );
   });
 });
+
+describe('pruneDeprecatedBundledExtensions', () => {
+  it('removes deprecated bundled extensions', async () => {
+    const removeExtensionFn = vi.fn().mockResolvedValue(undefined);
+    const existingExtensions = [
+      {
+        name: 'old-bundled-extension',
+        type: 'builtin',
+        description: 'Old bundled extension',
+        enabled: true,
+        bundled: true,
+      },
+    ] as FixedExtensionEntry[];
+
+    const remainingExtensions = await pruneDeprecatedBundledExtensions(
+      existingExtensions,
+      removeExtensionFn
+    );
+
+    expect(removeExtensionFn).toHaveBeenCalledWith('old-bundled-extension');
+    expect(remainingExtensions).toEqual([]);
+  });
+
+  it('does not remove non-bundled deprecated extensions', async () => {
+    const removeExtensionFn = vi.fn().mockResolvedValue(undefined);
+    const existingExtensions = [
+      {
+        name: 'old-bundled-extension',
+        type: 'builtin',
+        description: 'Old bundled extension',
+        enabled: true,
+        bundled: false,
+      },
+    ] as FixedExtensionEntry[];
+
+    const remainingExtensions = await pruneDeprecatedBundledExtensions(
+      existingExtensions,
+      removeExtensionFn
+    );
+
+    expect(removeExtensionFn).not.toHaveBeenCalled();
+    expect(remainingExtensions).toEqual(existingExtensions);
+  });
+
+  it('allows same-id bundled extensions to be re-added after prune', async () => {
+    const removeExtensionFn = vi.fn().mockResolvedValue(undefined);
+    const addExtensionFn = vi.fn().mockResolvedValue(undefined);
+    const existingExtensions = [
+      {
+        name: 'Google Drive',
+        type: 'stdio',
+        description: 'Google Drive extension',
+        cmd: 'some-cmd',
+        args: [],
+        env_keys: [],
+        enabled: true,
+        bundled: true,
+      },
+    ] as FixedExtensionEntry[];
+
+    const remainingExtensions = await pruneDeprecatedBundledExtensions(
+      existingExtensions,
+      removeExtensionFn
+    );
+
+    await syncBundledExtensions(remainingExtensions, addExtensionFn);
+
+    expect(removeExtensionFn).toHaveBeenCalledWith('googledrive');
+    expect(addExtensionFn).toHaveBeenCalledWith(
+      'googledrive',
+      expect.objectContaining({
+        type: 'stdio',
+        name: 'googledrive',
+        bundled: true,
+      }),
+      true
+    );
+  });
+});
diff --git a/ui/desktop/src/components/settings/extensions/bundled-extensions.ts b/ui/desktop/src/components/settings/extensions/bundled-extensions.ts
index a04ad5b8..332d1dfb 100644
--- a/ui/desktop/src/components/settings/extensions/bundled-extensions.ts
+++ b/ui/desktop/src/components/settings/extensions/bundled-extensions.ts
@@ -1,6 +1,7 @@
 import type { ExtensionConfig } from '../../../api/types.gen';
 import { FixedExtensionEntry } from '../../ConfigContext';
 import bundledExtensionsData from './bundled-extensions.json';
+import deprecatedBundledExtensionsData from './deprecated-bundled-extensions.json';
 import { nameToKey } from './utils';
 
 // Type definition for built-in extensions from JSON
@@ -20,28 +21,40 @@ type BundledExtension = {
   allow_configure?: boolean;
 };
 
-const DEPRECATED_GOOGLE_DRIVE_IDS = ['googledrive', 'google_drive'];
-const DEPRECATED_GOOGLE_DRIVE_ENV_KEYS = [
-  'GOOGLE_DRIVE_CREDENTIALS_PATH',
-  'GOOGLE_DRIVE_OAUTH_PATH',
-];
+type DeprecatedBundledExtension = {
+  id: string;
+};
 
-export function isDeprecatedGoogleDriveExtension(ext: FixedExtensionEntry): boolean {
-  if (!DEPRECATED_GOOGLE_DRIVE_IDS.includes(nameToKey(ext.name))) {
-    return false;
+export function getDeprecatedBundledExtensions(): DeprecatedBundledExtension[] {
+  return deprecatedBundledExtensionsData as DeprecatedBundledExtension[];
+}
+
+function isBundledExtension(extension: FixedExtensionEntry): boolean {
+  return 'bundled' in extension && extension.bundled === true;
+}
+
+export async function pruneDeprecatedBundledExtensions(
+  existingExtensions: FixedExtensionEntry[],
+  removeExtensionFn: (id: string) => Promise<void>
+): Promise<FixedExtensionEntry[]> {
+  const deprecatedExtensionIds = new Set(getDeprecatedBundledExtensions().map((ext) => ext.id));
+  const remainingExtensions: FixedExtensionEntry[] = [];
+
+  for (const existingExt of existingExtensions) {
+    if (!isBundledExtension(existingExt)) {
+      remainingExtensions.push(existingExt);
+      continue;
+    }
+
+    if (!deprecatedExtensionIds.has(nameToKey(existingExt.name))) {
+      remainingExtensions.push(existingExt);
+      continue;
+    }
+
+    await removeExtensionFn(nameToKey(existingExt.name));
   }
-  if (ext.type === 'builtin') {
-    return true;
-  }
-  if (
-    ext.type === 'stdio' &&
-    'env_keys' in ext &&
-    Array.isArray(ext.env_keys) &&
-    ext.env_keys.some((key: string) => DEPRECATED_GOOGLE_DRIVE_ENV_KEYS.includes(key))
-  ) {
-    return true;
-  }
-  return false;
+
+  return remainingExtensions;
 }
 
 /**
@@ -66,14 +79,7 @@ export async function syncBundledExtensions(
       // Find if this extension already exists
       const existingExt = existingExtensions.find((ext) => nameToKey(ext.name) === bundledExt.id);
 
-      // Skip if extension exists and is already marked as bundled, except when
-      // we must migrate deprecated extensions.
-      if (
-        existingExt &&
-        'bundled' in existingExt &&
-        existingExt.bundled &&
-        !isDeprecatedGoogleDriveExtension(existingExt)
-      ) {
+      if (existingExt && isBundledExtension(existingExt)) {
         continue;
       }
 
@@ -123,14 +129,3 @@ export async function syncBundledExtensions(
     throw error;
   }
 }
-
-/**
- * Function to initialize all built-in extensions for a first-time user.
- * This can be called when the application is first installed.
- */
-export async function initializeBundledExtensions(
-  addExtensionFn: (name: string, config: ExtensionConfig, enabled: boolean) => Promise<void>
-): Promise<void> {
-  // Call with an empty list to ensure all built-ins are added
-  await syncBundledExtensions([], addExtensionFn);
-}
diff --git a/ui/desktop/src/components/settings/extensions/deprecated-bundled-extensions.json b/ui/desktop/src/components/settings/extensions/deprecated-bundled-extensions.json
new file mode 100644
index 00000000..fe51488c
--- /dev/null
+++ b/ui/desktop/src/components/settings/extensions/deprecated-bundled-extensions.json
@@ -0,0 +1 @@
+[]
diff --git a/ui/desktop/src/components/settings/extensions/index.ts b/ui/desktop/src/components/settings/extensions/index.ts
index 67d0dc16..12f806ef 100644
--- a/ui/desktop/src/components/settings/extensions/index.ts
+++ b/ui/desktop/src/components/settings/extensions/index.ts
@@ -6,7 +6,7 @@ export {
   deleteExtension,
 } from './extension-manager';
 
-export { syncBundledExtensions, initializeBundledExtensions } from './bundled-extensions';
+export { pruneDeprecatedBundledExtensions, syncBundledExtensions } from './bundled-extensions';
 
 export { addExtensionFromDeepLink } from './deeplink';