diff --git a/server/src/main/java/com/linecorp/centraldogma/server/internal/replication/ZooKeeperCommandExecutor.java b/server/src/main/java/com/linecorp/centraldogma/server/internal/replication/ZooKeeperCommandExecutor.java
index 9b8bde90e..06408968f 100644
--- a/server/src/main/java/com/linecorp/centraldogma/server/internal/replication/ZooKeeperCommandExecutor.java
+++ b/server/src/main/java/com/linecorp/centraldogma/server/internal/replication/ZooKeeperCommandExecutor.java
@@ -680,14 +680,21 @@ private void stopLater() {
     protected void doStop(@Nullable Runnable onReleaseLeadership,
                           @Nullable Runnable onReleaseZoneLeadership) throws Exception {
         canReplicate = false;
+        // Stop accepting new replay logs.
         listenerInfo = null;
+
         logger.info("Stopping the worker threads");
         boolean interrupted = shutdown(executor);
         logger.info("Stopped the worker threads");
 
         try {
-            logger.info("Stopping the delegate command executor");
-            delegate.stop();
+            // A replay holds this monitor until it records its progress; close() would interrupt it.
+            logger.info("Waiting for an in-flight replay to finish");
+            synchronized (this) {
+                logger.info("No replay in flight; last replayed revision: {}", lastReplayedRevision);
+                logger.info("Stopping the delegate command executor");
+                delegate.stop();
+            }
             logger.info("Stopped the delegate command executor");
         } catch (Exception e) {
             logger.warn("Failed to stop the delegate command executor {}: {}", delegate, e.getMessage(), e);
@@ -817,7 +824,9 @@ private synchronized void replayLogs(long targetRevision, boolean force) {
                 l = loadLog(nextRevision);
                 final Command<?> command = l.command();
                 final Object expectedResult = l.result();
-                final Object actualResult = delegate.execute(REPLAY_CONTEXT, command).get();
+                // An interrupt here would split the local apply from updateLastReplayedRevision() below.
+                final Object actualResult =
+                        Uninterruptibles.getUninterruptibly(delegate.execute(REPLAY_CONTEXT, command));
 
                 if (!Objects.equals(expectedResult, actualResult)) {
                     throw new ReplicationException(
diff --git a/server/src/test/java/com/linecorp/centraldogma/server/internal/replication/ZooKeeperCommandExecutorTest.java b/server/src/test/java/com/linecorp/centraldogma/server/internal/replication/ZooKeeperCommandExecutorTest.java
index 6fddc42d4..10d25fe49 100644
--- a/server/src/test/java/com/linecorp/centraldogma/server/internal/replication/ZooKeeperCommandExecutorTest.java
+++ b/server/src/test/java/com/linecorp/centraldogma/server/internal/replication/ZooKeeperCommandExecutorTest.java
@@ -748,6 +748,68 @@ void inFlightCommandOnStopIsRecordedAndNotReplayed() throws Exception {
         }
     }
 
+    /**
+     * A replay still in flight when the executor stops must finish and record its progress durably,
+     * because closing the log watcher cancels its tasks with an interrupt. Otherwise the command is
+     * applied to the local data while last_revision is not advanced, and the next start-up applies it
+     * a second time.
+     */
+    @Test
+    @Timeout(120)
+    void inFlightReplayOnStopIsRecordedAndNotReplayed() throws Exception {
+        final CountDownLatch replayEntered = new CountDownLatch(1);
+        final CountDownLatch proceed = new CountDownLatch(1);
+        final AtomicInteger replayCount = new AtomicInteger();
+        final AtomicInteger replicaIndex = new AtomicInteger();
+        final Supplier<Function<Command<?>, CompletableFuture<?>>> delegateSupplier = () -> {
+            final boolean replaying = replicaIndex.getAndIncrement() == 1;
+            final Function<Command<?>, CompletableFuture<?>> base = newMockDelegate();
+            return command -> {
+                if (replaying && command != null && command.type() == CommandType.CREATE_REPOSITORY) {
+                    // Park inside replayLogs() so we can stop while the replay is in flight.
+                    replayCount.incrementAndGet();
+                    replayEntered.countDown();
+                    return CompletableFuture.supplyAsync(() -> {
+                        try {
+                            proceed.await();
+                        } catch (InterruptedException e) {
+                            throw new RuntimeException(e);
+                        }
+                        return null;
+                    }, CommonPools.blockingTaskExecutor());
+                }
+                return base.apply(command);
+            };
+        };
+
+        try (Cluster cluster = Cluster.builder().numReplicas(3).build(delegateSupplier)) {
+            final Replica origin = cluster.get(0);
+            final Replica replaying = cluster.get(1);
+            origin.commandExecutor().execute(Command.createProject(Author.SYSTEM, "p")).join();
+            await().untilAsserted(() -> assertThat(replaying.localRevision()).isEqualTo(0L));
+
+            // Park the replay of revision 1, then stop while it is in flight.
+            origin.commandExecutor().execute(Command.createRepository(Author.SYSTEM, "p", "r")).join();
+            assertThat(replayEntered.await(10, TimeUnit.SECONDS)).isTrue();
+            final CompletableFuture<Void> stopFuture = replaying.commandExecutor().stop();
+            // The shutdown must not finish while the replay is parked; that is the barrier doing its job.
+            assertThatThrownBy(() -> stopFuture.get(3, TimeUnit.SECONDS))
+                    .isInstanceOf(TimeoutException.class);
+            proceed.countDown();
+            stopFuture.join();
+
+            // The replay finished before the log watcher was closed, so its progress is durable.
+            assertThat(replaying.localRevision()).isEqualTo(1L);
+
+            // Catch up on a later revision to prove revision 1 was not applied a second time.
+            replaying.commandExecutor().start().join();
+            origin.commandExecutor().execute(Command.createProject(Author.SYSTEM, "p2")).join();
+            await().untilAsserted(() -> assertThat(replaying.localRevision()).isEqualTo(2L));
+            assertThat(replayCount).hasValue(1);
+            assertThat(replaying.commandExecutor().isWritable()).isTrue();
+        }
+    }
+
     private static <T> void awaitUntilReplicated(Cluster cluster, Command<T> command) {
         for (int i = 0; i < cluster.size(); i++) {
             final Replica replica = cluster.get(i);