If you’ve been struggling with songs disappearing after a sync, or your entire library never making it to your iPhone, you’re dealing with one of the most persistent annoyances in the Apple ecosystem. The sync can stall with messages like “waiting for changes to be applied” or “waiting to copy items,” or skip tracks silently with no explanation. Either way, the problem is almost always fixable.
One thing to know upfront: on Mac, iTunes is gone. Device syncing lives in Finder, and your music library lives in the Music app. On Windows, iTunes is still the tool. This article covers both, plus cloud-based syncing via Sync Library if you use Apple Music or iTunes Match.
Quick Checks Before You Start
Run through these first. They solve more problems than you’d expect.
- Update your iPhone, Mac (or Windows PC), and iTunes (Windows only) to the latest versions. Apple links specific sync errors, including -5000, -69, 13010, and 13014, directly to outdated software.
- Confirm your iPhone has free space. Go to Settings > General > iPhone Storage. A full device silently skips songs during sync.
- Try a different USB-C cable or Lightning cable. A worn or flaky cable is behind more mysterious sync failures than anything else.
- Check Apple’s System Status page to rule out an iCloud Music or iTunes Store outage.
- Restart both your computer and iPhone before retrying a sync.
Sync Your Entire Music Library from Mac (Finder)
Connect your iPhone to your Mac, then open Finder. Your iPhone appears under Locations in the left sidebar.
- Click your iPhone’s name in the sidebar.
- If you see a Trust prompt in Finder, click it, and tap Trust on your iPhone, then enter your passcode.
- At the top of the Finder pane, click the Music tab.
- Check Sync music onto “[your iPhone]”.
- Select Entire music library, or pick Selected playlists, artists, albums, and genres if storage is tight.
- Click Apply, then Sync.
Don’t disconnect until the progress indicator in the Finder toolbar disappears. Pulling the cable mid-sync can corrupt the transfer and leave you with an incomplete library.
Sync Your Music Library from Windows (iTunes)
- Update iTunes to the latest version via the Microsoft Store or Apple’s website.
- Connect your iPhone via USB.
- Open iTunes and click the device icon near the top-left corner.
- In the left sidebar, select Music under your device.
- Check Sync Music.
- Choose Entire music library, or narrow it to specific playlists and artists.
- Click Apply, then Sync.
Wait for the progress bar to clear before disconnecting. A powered USB hub can help if you’re getting intermittent drops with a USB-A port.
Use Sync Library (Apple Music and iTunes Match)
Sync Library handles music across all your devices over iCloud, no cable required. If you subscribe to Apple Music or iTunes Match, it uploads your local tracks and makes them available everywhere.
The trade-off: when Sync Library is on, it manages your library and can override manual cable-based transfers. If you want to push music by cable, turn Sync Library off first (covered in the troubleshooting section below).
On iPhone
Go to Settings > Music and turn on Sync Library.
If the toggle isn’t there, your Apple ID doesn’t have an active Apple Music or iTunes Match subscription. No subscription, no Sync Library.
On Mac (Music app)
- Open the Music app.
- Go to Music > Settings in the menu bar.
- On the General tab, check Sync Library and click OK.
To force a refresh, go to File > Library > Update Cloud Library.
On Windows (iTunes)
- Open iTunes, then go to Edit > Preferences.
- On the General tab, check Sync Library, the label may read “iCloud Music Library” depending on your iTunes version.
- Click OK.
- To force a refresh, go to File > Library > Update iCloud Music Library.
Large libraries take time. Watch the status bar at the bottom of the Music sidebar for “Updating Cloud Library”, it’ll clear when it’s done.
Troubleshooting: Why Songs Are Still Missing
Consolidate your library
If the Music app or iTunes can’t find a file on disk, it skips that track without warning. Songs with a broken file reference show an exclamation mark (!) next to the title.
On Mac: in the Music app, go to File > Library > Organize Library, check Consolidate files, and click OK. This copies all referenced tracks into one folder so nothing gets skipped.
On Windows: same path in iTunes, File > Library > Organize Library > Consolidate files.
Retry your sync after consolidating.
Fix or remove songs with broken file paths
Click any song marked with a ! to see if Music or iTunes can locate it. If it can’t, right-click and use the option to find the file manually, point it to the correct location on your drive. If the file is genuinely gone, remove the entry from your library. Broken references block clean syncs.
Check for DRM and unsupported formats
Tracks with DRM restrictions, or files in formats like FLAC, OGG, or WMA, often won’t transfer to iPhone through standard sync. Convert problem files to AAC or MP3 via File > Convert in the Music app or iTunes. Third-party music transfer utilities handle non-Apple formats much better if you have a large collection in those formats.
Resolve the Sync Library vs. cable sync conflict
When Sync Library is on, the cloud library takes priority and manual cable-based transfers can be blocked or reversed. Turn off Sync Library on both your iPhone (Settings > Music) and your Mac (Music app Settings > General) before doing a cable sync. Re-enable it afterward if you want cloud sync to resume.
Verify your Apple ID
Purchased songs not appearing is almost always an Apple ID mismatch. On your iPhone, go to Settings > [your name] and confirm you’re signed in with the same Apple ID used to buy or subscribe to music. Sign out and back in if there’s any doubt. On Mac, check Music app > Account to confirm the same account is active there.
Diagnose a stuck sync
If Finder or iTunes gets frozen on “waiting for changes to be applied” or “waiting to copy items,” the usual culprits are:
- A corrupted file in the queue: consolidate your library and remove tracks with ! markers before retrying.
- Low device storage: free up space on the iPhone before starting the sync again.
- Security software on Windows: antivirus or firewall tools sometimes block iTunes from reaching Apple’s servers. Temporarily disable them during sync to test.
- A bad USB connection: swap in a different USB-C cable or try a different port on your computer.
Reset network settings (for persistent Sync Library failures)
If Sync Library keeps stalling and your internet connection is otherwise fine, go to Settings > General > Transfer or Reset iPhone > Reset > Reset Network Settings on your iPhone. This clears saved Wi-Fi passwords and VPN configs, so have those ready before you tap it.
After it restarts, reconnect to Wi-Fi and try Sync Library again.
Alternatives When Standard Sync Keeps Failing
Download directly in the Music app
If all the music you want is on Apple Music, cable sync is optional. Open the Music app on your iPhone, find the albums or playlists you want, and tap the download icon. Everything goes straight to the device without touching a computer.
Third-party transfer tools
Several utilities move music to iPhone over USB without going through Finder or iTunes, useful if you’re dealing with large FLAC or OGG collections, or if the standard sync tools keep choking on your library. They typically give you drag-and-drop control and don’t interact with Sync Library at all.
If you’ve run through all of this and specific tracks are still missing, right-click them in the Music app or iTunes and check their status. Tracks flagged as “Ineligible” can’t be uploaded to iCloud, usually because of DRM, an unsupported format, or file corruption. Replacing or converting those files is the only fix. Everything else covered above should be resolved.