diff --git a/packages/server/src/utils/checkout-git.test.ts b/packages/server/src/utils/checkout-git.test.ts
index c28586d8a..9c319ca54 100644
--- a/packages/server/src/utils/checkout-git.test.ts
+++ b/packages/server/src/utils/checkout-git.test.ts
@@ -315,18 +315,28 @@ describe("checkout git utilities", () => {
     });
   });
 
-  it("reports a real non-git directory as non-git", async () => {
+  it("reports an ordinary directory as non-git without warning", async () => {
     const nonGitDir = join(tempDir, "not-git-status");
     mkdirSync(nonGitDir, { recursive: true });
+    const records: unknown[] = [];
+    const logger = pino(
+      { level: "warn" },
+      {
+        write(line: string) {
+          records.push(JSON.parse(line));
+        },
+      },
+    );
 
-    await expect(getCheckoutStatus(nonGitDir)).resolves.toEqual({ isGit: false });
+    await expect(getCheckoutStatus(nonGitDir, { logger })).resolves.toEqual({ isGit: false });
+    expect(records).toEqual([]);
   });
 
   it.runIf(
     process.platform !== "win32" &&
       existsSync("/dev/shm") &&
       statSync("/dev").dev !== statSync("/dev/shm").dev,
-  )("warns and reports a non-git directory at a filesystem boundary as non-git", async () => {
+  )("does not warn for a non-git directory at a filesystem boundary", async () => {
     const nonGitDir = realpathSync.native(mkdtempSync("/dev/shm/checkout-git-boundary-test-"));
     const records: unknown[] = [];
     const logger = pino(
@@ -339,21 +349,34 @@ describe("checkout git utilities", () => {
     );
     try {
       await expect(getCheckoutStatus(nonGitDir, { logger })).resolves.toEqual({ isGit: false });
-      expect(records).toEqual([
-        expect.objectContaining({
-          level: 40,
-          cwd: nonGitDir,
-          msg: "Git worktree discovery failed; treating directory as non-Git",
-          err: expect.objectContaining({
-            message: expect.stringContaining("Stopping at filesystem boundary"),
-          }),
-        }),
-      ]);
+      expect(records).toEqual([]);
     } finally {
       rmSync(nonGitDir, { recursive: true, force: true });
     }
   });
 
+  it("warns when git discovery fails unexpectedly", async () => {
+    const missingDir = join(tempDir, "missing-git-cwd");
+    const records: unknown[] = [];
+    const logger = pino(
+      { level: "warn" },
+      {
+        write(line: string) {
+          records.push(JSON.parse(line));
+        },
+      },
+    );
+
+    await expect(getCheckoutStatus(missingDir, { logger })).resolves.toEqual({ isGit: false });
+    expect(records).toEqual([
+      expect.objectContaining({
+        level: 40,
+        cwd: missingDir,
+        msg: "Git worktree discovery failed; treating directory as non-Git",
+      }),
+    ]);
+  });
+
   it("returns null for getCurrentBranch in a repo with no commits", async () => {
     const emptyRepo = join(tempDir, "empty-repo");
     mkdirSync(emptyRepo, { recursive: true });
diff --git a/packages/server/src/utils/checkout-git.ts b/packages/server/src/utils/checkout-git.ts
index 1b0752ede..ed026e70c 100644
--- a/packages/server/src/utils/checkout-git.ts
+++ b/packages/server/src/utils/checkout-git.ts
@@ -810,6 +810,10 @@ export type CheckoutSnapshotFacts =
       pullRequestLookupTarget: PullRequestStatusLookupTarget | null;
     };
 
+function isNotGitRepositoryError(error: unknown): boolean {
+  return error instanceof Error && /not a git repository/i.test(error.message);
+}
+
 async function requireGitRepo(cwd: string): Promise<void> {
   try {
     await runGitCommand(["rev-parse", "--git-dir"], { cwd, envOverlay: READ_ONLY_GIT_ENV });
@@ -897,11 +901,12 @@ async function getWorktreeRoot(cwd: string, context?: CheckoutContext): Promise<
     });
     return parseGitRevParsePath(stdout);
   } catch (error) {
-    // Git discovery is fail-open: keep the directory usable as non-Git and retain the diagnostic.
-    context?.logger?.warn(
-      { err: error, cwd },
-      "Git worktree discovery failed; treating directory as non-Git",
-    );
+    if (!isNotGitRepositoryError(error)) {
+      context?.logger?.warn(
+        { err: error, cwd },
+        "Git worktree discovery failed; treating directory as non-Git",
+      );
+    }
     return null;
   }
 }