diff --git a/ui/desktop/src/App.tsx b/ui/desktop/src/App.tsx
index 2531c3940805..ba03ed6dc576 100644
--- a/ui/desktop/src/App.tsx
+++ b/ui/desktop/src/App.tsx
@@ -83,23 +83,17 @@ const PairRouteWrapper = ({
   const [isCreatingSession, setIsCreatingSession] = useState(false);
 
   const resumeSessionId = searchParams.get('resumeSessionId') ?? undefined;
-  const recipeId = searchParams.get('recipeId') ?? undefined;
   const recipeDeeplinkFromConfig = window.appConfig?.get('recipeDeeplink') as string | undefined;
   const initialMessage = routeState.initialMessage;
 
-  // Create session if we have an initialMessage, recipeId, or recipeDeeplink but no sessionId
+  // Create session if we have an initialMessage or recipeDeeplink but no sessionId
   useEffect(() => {
-    if (
-      (initialMessage || recipeId || recipeDeeplinkFromConfig) &&
-      !resumeSessionId &&
-      !isCreatingSession
-    ) {
+    if ((initialMessage || recipeDeeplinkFromConfig) && !resumeSessionId && !isCreatingSession) {
       setIsCreatingSession(true);
 
       (async () => {
         try {
           const newSession = await createSession(getInitialWorkingDir(), {
-            recipeId,
             recipeDeeplink: recipeDeeplinkFromConfig,
             allExtensions: extensionsList,
           });
@@ -115,7 +109,6 @@ const PairRouteWrapper = ({
 
           setSearchParams((prev) => {
             prev.set('resumeSessionId', newSession.id);
-            prev.delete('recipeId');
             return prev;
           });
         } catch (error) {
@@ -133,14 +126,7 @@ const PairRouteWrapper = ({
     // Note: isCreatingSession is intentionally NOT in the dependency array
     // It's only used as a guard to prevent concurrent session creation
     // eslint-disable-next-line react-hooks/exhaustive-deps
-  }, [
-    initialMessage,
-    recipeId,
-    recipeDeeplinkFromConfig,
-    resumeSessionId,
-    setSearchParams,
-    extensionsList,
-  ]);
+  }, [initialMessage, recipeDeeplinkFromConfig, resumeSessionId, setSearchParams, extensionsList]);
 
   // Add resumed session to active sessions if not already there
   useEffect(() => {
diff --git a/ui/desktop/src/components/bottom_menu/BottomMenuExtensionSelection.tsx b/ui/desktop/src/components/bottom_menu/BottomMenuExtensionSelection.tsx
index dc2266f59a4b..d4368ac6b9d2 100644
--- a/ui/desktop/src/components/bottom_menu/BottomMenuExtensionSelection.tsx
+++ b/ui/desktop/src/components/bottom_menu/BottomMenuExtensionSelection.tsx
@@ -40,11 +40,17 @@ export const BottomMenuExtensionSelection = ({ sessionId }: BottomMenuExtensionS
       }, 500);
     };
 
+    const handleExtensionsLoaded = () => {
+      setRefreshTrigger((prev) => prev + 1);
+    };
+
     window.addEventListener(AppEvents.SESSION_CREATED, handleSessionLoaded);
+    window.addEventListener(AppEvents.SESSION_EXTENSIONS_LOADED, handleExtensionsLoaded);
     window.addEventListener(AppEvents.MESSAGE_STREAM_FINISHED, handleSessionLoaded);
 
     return () => {
       window.removeEventListener(AppEvents.SESSION_CREATED, handleSessionLoaded);
+      window.removeEventListener(AppEvents.SESSION_EXTENSIONS_LOADED, handleExtensionsLoaded);
       window.removeEventListener(AppEvents.MESSAGE_STREAM_FINISHED, handleSessionLoaded);
     };
   }, []);
diff --git a/ui/desktop/src/components/recipes/RecipesView.tsx b/ui/desktop/src/components/recipes/RecipesView.tsx
index 5390c5984e5f..b7c2a8138024 100644
--- a/ui/desktop/src/components/recipes/RecipesView.tsx
+++ b/ui/desktop/src/components/recipes/RecipesView.tsx
@@ -32,7 +32,7 @@ import {
 } from '../../api';
 import ImportRecipeForm, { ImportRecipeButton } from './ImportRecipeForm';
 import CreateEditRecipeModal from './CreateEditRecipeModal';
-import { generateDeepLink, Recipe, stripEmptyExtensions } from '../../recipe';
+import { generateDeepLink, encodeRecipe, Recipe, stripEmptyExtensions } from '../../recipe';
 import { useNavigation } from '../../hooks/useNavigation';
 import { CronPicker } from '../schedule/CronPicker';
 import { Dialog, DialogContent, DialogHeader, DialogTitle } from '../ui/dialog';
@@ -165,15 +165,16 @@ export default function RecipesView() {
     }
   };
 
-  const handleStartRecipeChatInNewWindow = (recipeId: string) => {
+  const handleStartRecipeChatInNewWindow = async (recipe: Recipe) => {
     try {
+      const encodedRecipe = await encodeRecipe(stripEmptyExtensions(recipe) as Recipe);
       window.electron.createChatWindow(
         undefined,
         getInitialWorkingDir(),
         undefined,
         undefined,
         'pair',
-        recipeId
+        encodedRecipe
       );
       trackRecipeStarted(true, undefined, true);
     } catch (error) {
@@ -521,7 +522,7 @@ export default function RecipesView() {
           <Button
             onClick={(e) => {
               e.stopPropagation();
-              handleStartRecipeChatInNewWindow(recipeManifestResponse.id);
+              handleStartRecipeChatInNewWindow(recipe);
             }}
             variant="outline"
             size="sm"
diff --git a/ui/desktop/src/constants/events.ts b/ui/desktop/src/constants/events.ts
index c4a250fa5aee..69f26aeb2c23 100644
--- a/ui/desktop/src/constants/events.ts
+++ b/ui/desktop/src/constants/events.ts
@@ -3,6 +3,7 @@
  */
 export enum AppEvents {
   SESSION_CREATED = 'session-created',
+  SESSION_EXTENSIONS_LOADED = 'session-extensions-loaded',
   SESSION_DELETED = 'session-deleted',
   SESSION_RENAMED = 'session-renamed',
   SESSION_FORKED = 'session-forked',
diff --git a/ui/desktop/src/main.ts b/ui/desktop/src/main.ts
index 5cd77fb8dc67..897430f68154 100644
--- a/ui/desktop/src/main.ts
+++ b/ui/desktop/src/main.ts
@@ -157,7 +157,6 @@ if (process.platform !== 'darwin') {
               undefined,
               deeplinkData?.config,
               scheduledJobId || undefined,
-              undefined,
               deeplinkData?.parameters
             );
           });
@@ -258,7 +257,6 @@ async function processProtocolUrl(parsedUrl: URL, window: BrowserWindow) {
       undefined,
       deeplinkData?.config,
       scheduledJobId || undefined,
-      undefined,
       deeplinkData?.parameters
     );
     pendingDeepLink = null;
@@ -297,7 +295,6 @@ app.on('open-url', async (_event, url) => {
         undefined,
         deeplinkData?.config,
         scheduledJobId || undefined,
-        undefined,
         deeplinkData?.parameters
       );
       windowDeeplinkURL = null;
@@ -480,7 +477,6 @@ const createChat = async (
   viewType?: string,
   recipeDeeplink?: string, // Raw deeplink decoded on server
   scheduledJobId?: string, // Scheduled job ID if applicable
-  recipeId?: string,
   recipeParameters?: Record<string, string> // Recipe parameter values from deeplink URL
 ) => {
   const settings = getSettings();
@@ -528,7 +524,6 @@ const createChat = async (
           REQUEST_DIR: dir,
           GOOSE_BASE_URL_SHARE: baseUrlShare,
           GOOSE_VERSION: version,
-          recipeId: recipeId,
           recipeDeeplink: recipeDeeplink,
           recipeParameters: recipeParameters,
           scheduledJobId: scheduledJobId,
@@ -711,10 +706,7 @@ const createChat = async (
   if (viewType) {
     appPath = routeMap[viewType] || '/';
   }
-  if (
-    appPath === '/' &&
-    (recipeDeeplink !== undefined || recipeId !== undefined || initialMessage)
-  ) {
+  if (appPath === '/' && (recipeDeeplink !== undefined || initialMessage)) {
     appPath = '/pair';
   }
 
@@ -725,14 +717,6 @@ const createChat = async (
       appPath = '/pair';
     }
   }
-  // Only add recipeId to URL for the non-deeplink case (saved recipes launched from UI)
-  // For deeplinks, the recipe object is passed via appConfig, not URL params
-  if (recipeId) {
-    searchParams.set('recipeId', recipeId);
-    if (appPath === '/') {
-      appPath = '/pair';
-    }
-  }
 
   // Goose's react app uses HashRouter, so the path + search params follow a #/
   url.hash = `${appPath}?${searchParams.toString()}`;
@@ -1064,7 +1048,6 @@ const openDirectoryDialog = async (): Promise<OpenDialogReturnValue> => {
       undefined,
       deeplinkData?.config,
       undefined,
-      undefined,
       deeplinkData?.parameters
     );
   }
@@ -2018,13 +2001,13 @@ async function appMain() {
 
   ipcMain.on(
     'create-chat-window',
-    (event, query, dir, version, resumeSessionId, viewType, recipeId) => {
+    (event, query, dir, version, resumeSessionId, viewType, recipeDeeplink) => {
       if (!dir?.trim()) {
         const recentDirs = loadRecentDirs();
         dir = recentDirs.length > 0 ? recentDirs[0] : undefined;
       }
 
-      const isFromLauncher = query && !resumeSessionId && !viewType && !recipeId;
+      const isFromLauncher = query && !resumeSessionId && !viewType && !recipeDeeplink;
 
       if (isFromLauncher) {
         const senderWindow = BrowserWindow.fromWebContents(event.sender);
@@ -2052,9 +2035,9 @@ async function appMain() {
         version,
         resumeSessionId,
         viewType,
+        recipeDeeplink,
         undefined,
-        undefined,
-        recipeId
+        undefined
       );
     }
   );
diff --git a/ui/desktop/src/preload.ts b/ui/desktop/src/preload.ts
index 59cd44afc9ce..185b7f6723f2 100644
--- a/ui/desktop/src/preload.ts
+++ b/ui/desktop/src/preload.ts
@@ -64,7 +64,7 @@ type ElectronAPI = {
     version?: string,
     resumeSessionId?: string,
     viewType?: string,
-    recipeId?: string
+    recipeDeeplink?: string
   ) => void;
   logInfo: (txt: string) => void;
   showNotification: (data: NotificationData) => void;
@@ -156,7 +156,7 @@ const electronAPI: ElectronAPI = {
     version?: string,
     resumeSessionId?: string,
     viewType?: string,
-    recipeId?: string
+    recipeDeeplink?: string
   ) =>
     ipcRenderer.send(
       'create-chat-window',
@@ -165,7 +165,7 @@ const electronAPI: ElectronAPI = {
       version,
       resumeSessionId,
       viewType,
-      recipeId
+      recipeDeeplink
     ),
   logInfo: (txt: string) => ipcRenderer.send('logInfo', txt),
   showNotification: (data: NotificationData) => ipcRenderer.send('notify', data),
diff --git a/ui/desktop/src/recipe/index.ts b/ui/desktop/src/recipe/index.ts
index 03a33985f95b..3c20c0ba9ab0 100644
--- a/ui/desktop/src/recipe/index.ts
+++ b/ui/desktop/src/recipe/index.ts
@@ -49,7 +49,7 @@ export async function decodeRecipe(deeplink: string): Promise<Recipe> {
       throw new Error('Decoded recipe is null');
     }
 
-    return response.data.recipe as Recipe;
+    return stripEmptyExtensions(response.data.recipe as Recipe);
   } catch (error) {
     console.error('Failed to decode deeplink:', error);
     throw error;
@@ -78,6 +78,19 @@ export async function generateDeepLink(recipe: Recipe): Promise<string> {
   return `goose://recipe?config=${encoded}`;
 }
 
+/**
+ * Strips empty extensions arrays from recipes before passing to the backend.
+ *
+ * This is a backwards compatibility workaround for the desktop app. Previously,
+ * the UI was saving recipes with an empty `extensions: []` array, which the
+ * backend interprets as "use no extensions" rather than "use user's default
+ * extensions". By removing the empty array, the backend will fall back to
+ * loading the user's configured default extensions.
+ *
+ * This can be removed once we have the ability to manage recipe extensions
+ * directly in the UI, allowing users to explicitly choose which extensions
+ * a recipe should use.
+ */
 export function stripEmptyExtensions(recipe: Recipe): Recipe {
   if (Array.isArray(recipe.extensions) && recipe.extensions.length === 0) {
     const { extensions: _, ...rest } = recipe;
diff --git a/ui/desktop/src/sessions.ts b/ui/desktop/src/sessions.ts
index 0ab2a45e9428..13c01096b506 100644
--- a/ui/desktop/src/sessions.ts
+++ b/ui/desktop/src/sessions.ts
@@ -7,6 +7,7 @@ import {
 } from './store/extensionOverrides';
 import type { FixedExtensionEntry } from './components/ConfigContext';
 import { AppEvents } from './constants/events';
+import { decodeRecipe, Recipe } from './recipe';
 
 export function shouldShowNewChatTitle(session: Session): boolean {
   if (session.recipe) {
@@ -36,7 +37,6 @@ export function resumeSession(session: Session, setView: setViewType) {
 export async function createSession(
   workingDir: string,
   options?: {
-    recipeId?: string;
     recipeDeeplink?: string;
     extensionConfigs?: ExtensionConfig[];
     allExtensions?: FixedExtensionEntry[];
@@ -44,17 +44,14 @@ export async function createSession(
 ): Promise<Session> {
   const body: {
     working_dir: string;
-    recipe_id?: string;
-    recipe_deeplink?: string;
+    recipe?: Recipe;
     extension_overrides?: ExtensionConfig[];
   } = {
     working_dir: workingDir,
   };
 
-  if (options?.recipeId) {
-    body.recipe_id = options.recipeId;
-  } else if (options?.recipeDeeplink) {
-    body.recipe_deeplink = options.recipeDeeplink;
+  if (options?.recipeDeeplink) {
+    body.recipe = await decodeRecipe(options.recipeDeeplink);
   }
 
   if (options?.extensionConfigs && options.extensionConfigs.length > 0) {
@@ -81,15 +78,15 @@ export async function startNewSession(
   setView: setViewType,
   workingDir: string,
   options?: {
-    recipeId?: string;
     recipeDeeplink?: string;
     allExtensions?: FixedExtensionEntry[];
   }
 ): Promise<Session> {
   const session = await createSession(workingDir, options);
-
-  // Include session data so sidebar can add it immediately (before it has messages)
   window.dispatchEvent(new CustomEvent(AppEvents.SESSION_CREATED, { detail: { session } }));
+  window.dispatchEvent(
+    new CustomEvent(AppEvents.SESSION_EXTENSIONS_LOADED, { detail: { session } })
+  );
 
   const initialMessage = initialText ? { msg: initialText, images: [] } : undefined;