diff --git a/apps/server/src/vcs/GitVcsDriver.test.ts b/apps/server/src/vcs/GitVcsDriver.test.ts
index 5ccc2c8c6b5bad8ffa706c1d2b9bf1515df55bd2..deb7c21b69920952ee6a1a898b316e37a202c060 100644
--- a/apps/server/src/vcs/GitVcsDriver.test.ts
+++ b/apps/server/src/vcs/GitVcsDriver.test.ts
@@ -623,3 +623,67 @@ it.effect("GitVcsDriver forwards execute env to the VCS process", () => {
     ),
   );
 });
+
+it.effect("GitVcsDriver flushes checkpoint objects and refs to disk before publishing them", () => {
+  const observedArgs: ReadonlyArray<string>[] = [];
+
+  return Effect.gen(function* () {
+    const driver = yield* GitVcsDriver.makeVcsDriverShape();
+
+    yield* driver.checkpoints.captureCheckpoint({
+      cwd: "/repo",
+      checkpointRef: CheckpointRef.make("refs/t3/checkpoints/thread/turn/1"),
+    });
+
+    const writeCommands = ["add", "write-tree", "commit-tree", "update-ref"];
+    const writes = observedArgs.filter((args) =>
+      writeCommands.some((command) => args.includes(command)),
+    );
+    assert.strictEqual(writes.length, 4);
+    for (const args of writes) {
+      const command = args.findIndex((arg) => writeCommands.includes(arg));
+      for (const setting of ["core.fsync=objects,reference", "core.fsyncMethod=fsync"]) {
+        const index = args.indexOf(setting);
+        assert.strictEqual(args[index - 1], "-c", args.join(" "));
+        assert.isBelow(index, command);
+      }
+    }
+    assert.deepStrictEqual(observedArgs.at(-1), [
+      "-C",
+      "/repo",
+      "-c",
+      "core.fsync=objects,reference",
+      "-c",
+      "core.fsyncMethod=fsync",
+      "update-ref",
+      "refs/t3/checkpoints/thread/turn/1",
+      "commit0000",
+    ]);
+  }).pipe(
+    Effect.provide(
+      Layer.mergeAll(
+        NodeServices.layer,
+        Layer.mock(VcsProcess.VcsProcess)({
+          run: (input) =>
+            Effect.sync(() => {
+              observedArgs.push(input.args);
+              const stdout = input.args.includes("write-tree")
+                ? "tree0000\n"
+                : input.args.includes("commit-tree")
+                  ? "commit0000\n"
+                  : input.args.includes("--git-common-dir")
+                    ? ".git\n"
+                    : "";
+              return {
+                exitCode: ChildProcessSpawner.ExitCode(0),
+                stdout,
+                stderr: "",
+                stdoutTruncated: false,
+                stderrTruncated: false,
+              };
+            }),
+        }),
+      ),
+    ),
+  );
+});
diff --git a/apps/server/src/vcs/GitVcsDriver.ts b/apps/server/src/vcs/GitVcsDriver.ts
index 3c6fbe04f89227bf03e13e1a011ef3ad05b3385e..50e63012f099b2e0d635fd05ce275bb00537032c 100644
--- a/apps/server/src/vcs/GitVcsDriver.ts
+++ b/apps/server/src/vcs/GitVcsDriver.ts
@@ -750,6 +750,17 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
       return path.isAbsolute(gitCommonDir) ? gitCommonDir : path.resolve(cwd, gitCommonDir);
     });
 
+  // Git renames loose objects and refs into place without fsync by default, so
+  // an unclean restart can leave 0-byte files under refs/t3/** that break every
+  // later fetch and push. Checkpoint writes flush before they are published;
+  // macOS defaults to writeout-only, which does not reach the disk either.
+  const durableWrite = [
+    "-c",
+    "core.fsync=objects,reference",
+    "-c",
+    "core.fsyncMethod=fsync",
+  ] as const;
+
   const checkpoints: VcsDriver.VcsCheckpointOps = {
     captureCheckpoint: Effect.fn("GitVcsDriver.checkpoints.captureCheckpoint")(function* (input) {
       const operation = "GitVcsDriver.checkpoints.captureCheckpoint";
@@ -907,14 +918,22 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
           operation,
           cwd: input.cwd,
           // Preserve absent skipped entries, but capture present nonignored files outside the cone.
-          args: [...indexConfig, "add", ...(sparseCheckout ? ["--sparse"] : []), "-A", "--", "."],
+          args: [
+            ...indexConfig,
+            ...durableWrite,
+            "add",
+            ...(sparseCheckout ? ["--sparse"] : []),
+            "-A",
+            "--",
+            ".",
+          ],
           env: commitEnv,
         });
 
         const writeTreeResult = yield* execute({
           operation,
           cwd: input.cwd,
-          args: [...indexConfig, "write-tree"],
+          args: [...indexConfig, ...durableWrite, "write-tree"],
           env: commitEnv,
         });
         const treeOid = writeTreeResult.stdout.trim();
@@ -932,7 +951,7 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
         const commitTreeResult = yield* execute({
           operation,
           cwd: input.cwd,
-          args: ["commit-tree", treeOid, "-m", message],
+          args: [...durableWrite, "commit-tree", treeOid, "-m", message],
           env: commitEnv,
         });
         const commitOid = commitTreeResult.stdout.trim();
@@ -949,7 +968,7 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
         yield* execute({
           operation,
           cwd: input.cwd,
-          args: ["update-ref", input.checkpointRef, commitOid],
+          args: [...durableWrite, "update-ref", input.checkpointRef, commitOid],
         });
       }).pipe(Effect.ensuring(cleanupTempIndex));
     }),