diff --git a/src/cli/commands/sync.ts b/src/cli/commands/sync.ts
index 197b4e5..cd5fa99 100644
--- a/src/cli/commands/sync.ts
+++ b/src/cli/commands/sync.ts
@@ -458,9 +458,8 @@ export async function syncApp() {
 
   console.log(`Syncing ${color.bold(appName)}...`)
 
-  // Initial sync: pull remote changes, then push local changes
-  await pullApp({ force: true, quiet: true })
-  await pushApp({ quiet: true })
+  // Initial sync: merge based on mtime, then push merged state
+  await mergeSync(appName)
 
   const gitignore = loadGitignore(process.cwd())
 
@@ -513,7 +512,7 @@ export async function syncApp() {
       for (const line of lines) {
         if (!line.startsWith('data: ')) continue
         if (pullTimer) clearTimeout(pullTimer)
-        pullTimer = setTimeout(() => pullApp({ force: true, quiet: true }), 500)
+        pullTimer = setTimeout(() => mergeSync(appName), 500)
       }
     }
   } finally {
@@ -881,6 +880,44 @@ function formatVersion(version: string): string {
   return date.toLocaleString()
 }
 
+async function mergeSync(appName: string): Promise<void> {
+  const diff = await getManifestDiff(appName)
+  if (!diff) return
+
+  const { changed, remoteOnly, localManifest, remoteManifest } = diff
+  if (!remoteManifest) return
+
+  // Determine which changed files to pull (remote is newer)
+  const toPull: string[] = [...remoteOnly]
+  for (const file of changed) {
+    const localMtime = new Date(localManifest.files[file]!.mtime).getTime()
+    const remoteMtime = new Date(remoteManifest.files[file]!.mtime).getTime()
+    if (remoteMtime > localMtime) {
+      toPull.push(file)
+    }
+  }
+
+  // Pull remote-newer and remote-only files
+  if (toPull.length > 0) {
+    for (const file of toPull) {
+      const content = await download(`/api/sync/apps/${appName}/files/${file}`)
+      if (!content) continue
+
+      const fullPath = join(process.cwd(), file)
+      const dir = dirname(fullPath)
+      if (!existsSync(dir)) {
+        mkdirSync(dir, { recursive: true })
+      }
+
+      writeFileSync(fullPath, content)
+      console.log(`  ${color.green('↓')} ${file}`)
+    }
+  }
+
+  // Push merged state to server
+  await pushApp({ quiet: true })
+}
+
 async function getManifestDiff(appName: string): Promise<ManifestDiff | null> {
   const localManifest = generateManifest(process.cwd(), appName)
   const result = await getManifest(appName)