diff --git a/packages/server/src/server/checkout-diff-manager.test.ts b/packages/server/src/server/checkout-diff-manager.test.ts
index bfbd4fd63..a14f0d386 100644
--- a/packages/server/src/server/checkout-diff-manager.test.ts
+++ b/packages/server/src/server/checkout-diff-manager.test.ts
@@ -115,6 +115,7 @@ describe("CheckoutDiffManager", () => {
     expect(workspaceGitService.getCheckoutDiff).toHaveBeenCalledWith(
       "/tmp/repo",
       expect.objectContaining({ mode: "uncommitted", includeStructured: true }),
+      undefined,
     );
   });
 
@@ -157,6 +158,49 @@ describe("CheckoutDiffManager", () => {
     });
   });
 
+  test("watch-triggered refresh forces a cache bypass on getCheckoutDiff", async () => {
+    const getCheckoutDiff = vi
+      .fn()
+      .mockResolvedValueOnce({
+        diff: "",
+        structured: [{ path: "a.ts", additions: 1, deletions: 0, status: "modified" }],
+      })
+      .mockResolvedValueOnce({
+        diff: "",
+        structured: [{ path: "b.ts", additions: 2, deletions: 0, status: "modified" }],
+      });
+
+    const { manager, getOnChange } = createManager({
+      getCheckoutDiffImplementation: getCheckoutDiff,
+    });
+
+    await manager.subscribe(
+      {
+        cwd: "/tmp/repo/packages/server",
+        compare: { mode: "uncommitted" },
+      },
+      vi.fn(),
+    );
+
+    expect(getCheckoutDiff).toHaveBeenNthCalledWith(
+      1,
+      "/tmp/repo",
+      expect.objectContaining({ mode: "uncommitted" }),
+      undefined,
+    );
+
+    const onChange = getOnChange();
+    onChange?.();
+    await vi.advanceTimersByTimeAsync(150);
+
+    expect(getCheckoutDiff).toHaveBeenCalledTimes(2);
+    const watchFiredCall = getCheckoutDiff.mock.calls[1];
+    expect(watchFiredCall[2]).toEqual({
+      force: true,
+      reason: expect.stringContaining("working-tree"),
+    });
+  });
+
   test("falls back to cwd when the working tree watch returns no repo root", async () => {
     const { manager, workspaceGitService } = createManager({ repoRoot: null });
 
@@ -171,6 +215,7 @@ describe("CheckoutDiffManager", () => {
     expect(workspaceGitService.getCheckoutDiff).toHaveBeenCalledWith(
       "/tmp/plain",
       expect.objectContaining({ mode: "uncommitted", includeStructured: true }),
+      undefined,
     );
   });
 });
diff --git a/packages/server/src/server/checkout-diff-manager.ts b/packages/server/src/server/checkout-diff-manager.ts
index 8f361ee2f..64a45c60e 100644
--- a/packages/server/src/server/checkout-diff-manager.ts
+++ b/packages/server/src/server/checkout-diff-manager.ts
@@ -164,16 +164,22 @@ export class CheckoutDiffManager {
   private async computeCheckoutDiffSnapshot(
     cwd: string,
     compare: CheckoutDiffCompareInput,
-    options?: { diffCwd?: string },
+    options?: { diffCwd?: string; force?: boolean; reason?: string },
   ): Promise<CheckoutDiffSnapshotPayload> {
     const diffCwd = options?.diffCwd ?? cwd;
     try {
-      const diffResult = await this.workspaceGitService.getCheckoutDiff(diffCwd, {
-        mode: compare.mode,
-        baseRef: compare.baseRef,
-        ignoreWhitespace: compare.ignoreWhitespace,
-        includeStructured: true,
-      });
+      const diffResult = await this.workspaceGitService.getCheckoutDiff(
+        diffCwd,
+        {
+          mode: compare.mode,
+          baseRef: compare.baseRef,
+          ignoreWhitespace: compare.ignoreWhitespace,
+          includeStructured: true,
+        },
+        options?.force
+          ? { force: true, reason: options.reason ?? "checkout-diff-refresh" }
+          : undefined,
+      );
       const files = [...(diffResult.structured ?? [])];
       files.sort((a, b) => {
         if (a.path === b.path) return 0;
@@ -204,6 +210,8 @@ export class CheckoutDiffManager {
         target.refreshQueued = false;
         const snapshot = await this.computeCheckoutDiffSnapshot(target.cwd, target.compare, {
           diffCwd: target.diffCwd,
+          force: true,
+          reason: "working-tree-watch",
         });
         target.latestPayload = snapshot;
         const fingerprint = JSON.stringify(snapshot);