diff --git a/apps/web/src/components/BranchToolbar.logic.test.ts b/apps/web/src/components/BranchToolbar.logic.test.ts
index 08e6f7633dee3..903a20066b39e 100644
--- a/apps/web/src/components/BranchToolbar.logic.test.ts
+++ b/apps/web/src/components/BranchToolbar.logic.test.ts
@@ -160,6 +160,18 @@ describe("dedupeRemoteBranchesWithLocalMatches", () => {
 
 describe("resolveBranchSelectionTarget", () => {
   it("reuses an existing secondary worktree for the selected ref", () => {
+    expect(
+      resolveBranchSelectionTarget({
+        activeProjectCwd: "/repo/nested-checkout/packages/app",
+        activeProjectCheckoutRoot: "/repo/nested-checkout",
+        activeWorktreePath: null,
+        refName: { isDefault: true, worktreePath: "/repo" },
+      }),
+    ).toEqual({
+      checkoutCwd: "/repo",
+      nextWorktreePath: "/repo",
+      reuseExistingWorktree: true,
+    });
     expect(
       resolveBranchSelectionTarget({
         activeProjectCwd: "/repo",
@@ -177,20 +189,31 @@ describe("resolveBranchSelectionTarget", () => {
   });
 
   it("switches back to the main repo when the ref already lives there", () => {
-    expect(
-      resolveBranchSelectionTarget({
-        activeProjectCwd: "/repo",
-        activeWorktreePath: "/repo/.t3/worktrees/feature-a",
-        refName: {
-          isDefault: true,
-          worktreePath: "/repo",
-        },
-      }),
-    ).toEqual({
-      checkoutCwd: "/repo",
-      nextWorktreePath: null,
-      reuseExistingWorktree: true,
-    });
+    // A subdirectory project's own checkout is reported at the repository root.
+    // The checkout root is undefined until the project's status loads.
+    for (const [activeProjectCwd, activeWorktreePath, activeProjectCheckoutRoot] of [
+      ["/repo", "/repo/.t3/worktrees/feature-a", "/repo"],
+      ["/repo/packages/app", "/repo/.t3/worktrees/feature-a", "/repo"],
+      ["/repo/packages/app", null, "/repo"],
+      ["/repo/packages/app", "/repo/.t3/worktrees/feature-a", undefined],
+      ["/repo/packages/app", null, undefined],
+    ] as const) {
+      expect(
+        resolveBranchSelectionTarget({
+          activeProjectCwd,
+          activeProjectCheckoutRoot,
+          activeWorktreePath,
+          refName: {
+            isDefault: true,
+            worktreePath: "/repo",
+          },
+        }),
+      ).toEqual({
+        checkoutCwd: "/repo",
+        nextWorktreePath: null,
+        reuseExistingWorktree: true,
+      });
+    }
   });
 
   it("keeps checkout in the current worktree for non-default refs", () => {
diff --git a/apps/web/src/components/BranchToolbar.logic.ts b/apps/web/src/components/BranchToolbar.logic.ts
index e22dcfaddedeb..a967c3171fbd1 100644
--- a/apps/web/src/components/BranchToolbar.logic.ts
+++ b/apps/web/src/components/BranchToolbar.logic.ts
@@ -7,6 +7,7 @@ import type {
 } from "@t3tools/contracts";
 import * as Schema from "effect/Schema";
 import { sanitizeNewRefName } from "@t3tools/shared/git";
+import { workspaceRelativeFilePath } from "@t3tools/shared/path";
 import { toSortableTimestamp } from "@t3tools/client-runtime/state/thread-sort";
 export { deriveLocalBranchNameFromRemoteRef, sanitizeNewRefName } from "@t3tools/shared/git";
 
@@ -247,6 +248,7 @@ export function resolveLocalCheckoutBranchMismatch(input: {
 
 export function resolveBranchSelectionTarget(input: {
   activeProjectCwd: string;
+  activeProjectCheckoutRoot?: string | undefined;
   activeWorktreePath: string | null;
   refName: Pick<VcsRef, "isDefault" | "worktreePath">;
 }): {
@@ -257,9 +259,14 @@ export function resolveBranchSelectionTarget(input: {
   const { activeProjectCwd, activeWorktreePath, refName } = input;
 
   if (refName.worktreePath) {
+    // Until the project's checkout root loads, a checkout containing the project counts as its own.
+    const isProjectCheckout =
+      input.activeProjectCheckoutRoot === undefined
+        ? workspaceRelativeFilePath(activeProjectCwd, refName.worktreePath) !== null
+        : workspaceRelativeFilePath(input.activeProjectCheckoutRoot, refName.worktreePath) === ".";
     return {
       checkoutCwd: refName.worktreePath,
-      nextWorktreePath: refName.worktreePath === activeProjectCwd ? null : refName.worktreePath,
+      nextWorktreePath: isProjectCheckout ? null : refName.worktreePath,
       reuseExistingWorktree: true,
     };
   }
diff --git a/apps/web/src/components/BranchToolbarBranchSelector.tsx b/apps/web/src/components/BranchToolbarBranchSelector.tsx
index fab250f6adaf8..9782f258afe19 100644
--- a/apps/web/src/components/BranchToolbarBranchSelector.tsx
+++ b/apps/web/src/components/BranchToolbarBranchSelector.tsx
@@ -224,6 +224,12 @@ export function BranchToolbarBranchSelector({
           input: { cwd: branchCwd },
         }),
   );
+  const projectStatusQuery = useEnvironmentQuery(
+    activeProjectCwd === null
+      ? null
+      : vcsEnvironment.status({ environmentId, input: { cwd: activeProjectCwd } }),
+  );
+  const activeProjectCheckoutRoot = projectStatusQuery.data?.workingTree.rootPath;
   const trimmedBranchQuery = branchQuery.trim();
   const branchRefState = usePaginatedBranches({
     environmentId,
@@ -389,6 +395,7 @@ export function BranchToolbarBranchSelector({
 
     const selectionTarget = resolveBranchSelectionTarget({
       activeProjectCwd,
+      activeProjectCheckoutRoot,
       activeWorktreePath,
       refName,
     });
@@ -631,6 +638,7 @@ export function BranchToolbarBranchSelector({
             (!activeProjectCwd ||
               !resolveBranchSelectionTarget({
                 activeProjectCwd,
+                activeProjectCheckoutRoot,
                 activeWorktreePath,
                 refName,
               }).reuseExistingWorktree))