diff --git a/packages/opencode/src/project/project.ts b/packages/opencode/src/project/project.ts
index 9870377b2169..d0cd84eb4e25 100644
--- a/packages/opencode/src/project/project.ts
+++ b/packages/opencode/src/project/project.ts
@@ -238,10 +238,19 @@ const layer = Layer.effect(
         vcs: data.vcs?.type ?? fakeVcs,
         time: { ...existing.time, updated: Date.now() },
       }
+      // Only add the directory as a sandbox when it is a genuine linked git
+      // worktree (common .git dir lives outside the working tree). Independent
+      // clones of the same remote share a project ID by design, but each clone
+      // is its own primary worktree and must NOT be treated as a sandbox of the
+      // first one — otherwise the front-end surfaces stale branch info from the
+      // first directory.
+      const isLinkedWorktree =
+        data.vcs?.type === "git" && !FSUtil.contains(data.directory, data.vcs.store)
       if (
         projectID !== ProjectV2.ID.global &&
         data.directory !== result.worktree &&
-        !result.sandboxes.includes(data.directory)
+        !result.sandboxes.includes(data.directory) &&
+        isLinkedWorktree
       )
         result.sandboxes.push(data.directory)
       result.sandboxes = yield* Effect.forEach(
diff --git a/packages/opencode/test/project/project.test.ts b/packages/opencode/test/project/project.test.ts
index 804b92b08ec4..8cef642ea486 100644
--- a/packages/opencode/test/project/project.test.ts
+++ b/packages/opencode/test/project/project.test.ts
@@ -362,6 +362,30 @@ describe("Project.fromDirectory with worktrees", () => {
     }),
   )
 
+  it.live("separate clones of the same repo should not add clone as sandbox", () =>
+    Effect.gen(function* () {
+      const project = yield* Project.Service
+      const tmp = yield* tmpdirScoped({ git: true })
+
+      // Create a bare remote, push, then clone into a second directory
+      const bare = tmp + "-bare"
+      const clone = tmp + "-clone"
+      yield* Effect.addFinalizer(() =>
+        Effect.promise(() => $`rm -rf ${bare} ${clone}`.quiet().nothrow()).pipe(Effect.ignore),
+      )
+      yield* Effect.promise(() => $`git clone --bare ${tmp} ${bare}`.quiet())
+      yield* Effect.promise(() => $`git clone ${bare} ${clone}`.quiet())
+
+      yield* project.fromDirectory(tmp)
+      const next = yield* project.fromDirectory(clone)
+
+      // The clone is an independent checkout, not a linked git worktree.
+      // It must NOT appear in sandboxes — otherwise the front-end surfaces
+      // stale branch info from the first directory.
+      expect(next.project.sandboxes).not.toContain(clone)
+    }),
+  )
+
   it.live("should accumulate multiple worktrees in sandboxes", () =>
     Effect.gen(function* () {
       const project = yield* Project.Service