diff --git a/apps/web/src/components/BranchToolbar.tsx b/apps/web/src/components/BranchToolbar.tsx
index f28aacac6174252eb3777705c59773abbd16a556..bc14843cf4c46180b6755a2fb00ab95a4668c21f 100644
--- a/apps/web/src/components/BranchToolbar.tsx
+++ b/apps/web/src/components/BranchToolbar.tsx
@@ -108,6 +108,12 @@ export default function BranchToolbar({ envMode, onEnvModeChange, envLocked }: B
 
   const setThreadBranch = (branch: string | null, worktreePath: string | null) => {
     if (!activeThreadId) return;
+    // If the effective cwd is about to change, stop the running session so the
+    // next message creates a new one with the correct cwd.
+    const sessionId = activeThread?.session?.sessionId;
+    if (sessionId && worktreePath !== activeWorktreePath) {
+      void api?.providers.stopSession({ sessionId }).catch(() => undefined);
+    }
     dispatch({ type: "SET_THREAD_BRANCH", threadId: activeThreadId, branch, worktreePath });
   };
 
diff --git a/apps/web/src/store.ts b/apps/web/src/store.ts
index 2ac4e173a8a95914d0f2a3f05799c7ee2b5260dc..a073c924289899daf7745e39785d76b056a983d3 100644
--- a/apps/web/src/store.ts
+++ b/apps/web/src/store.ts
@@ -376,15 +376,23 @@ export function reducer(state: AppState, action: Action): AppState {
         })),
       };
 
-    case "SET_THREAD_BRANCH":
+    case "SET_THREAD_BRANCH": {
       return {
         ...state,
-        threads: updateThread(state.threads, action.threadId, (t) => ({
-          ...t,
-          branch: action.branch,
-          worktreePath: action.worktreePath,
-        })),
+        threads: updateThread(state.threads, action.threadId, (t) => {
+          // When the effective cwd changes (worktreePath differs), the old
+          // session is no longer valid — clear it so ensureSession creates a
+          // new one with the correct cwd on the next message.
+          const cwdChanged = t.worktreePath !== action.worktreePath;
+          return {
+            ...t,
+            branch: action.branch,
+            worktreePath: action.worktreePath,
+            ...(cwdChanged ? { session: null } : {}),
+          };
+        }),
       };
+    }
 
     case "SET_RUNTIME_MODE":
       return {