Desktop Files Disappeared After Enabling iCloud?

You clicked something in iCloud settings, and now the Desktop is bare and Finder's sidebar looks rearranged. Nothing is deleted. Turning on Desktop & Documents Folders sync relocates those two folders into iCloud Drive — your files are all still there, one level away from where you left them.

Where the files went

With Desktop & Documents sync on, your Desktop and Documents folders stop living at ~/Desktop and ~/Documents and become folders inside iCloud Drive. Finder reflects the move: both folders now appear under the iCloud section of the sidebar rather than under Favorites.

1. Open a Finder window and click iCloud Drive in the sidebar.
2. Open the Desktop folder there. Your files are inside — and because it is your Desktop now, they also still show on the actual desktop behind your windows.
3. If the desktop looks empty anyway, check Finder isn't just hiding icons: click the desktop, then View → Show View Options, and make sure sorting hasn't stacked everything; also try ⌘F and search the file's name to confirm it exists.

Files may show a cloud icon while they upload or after they're evicted to save disk space — click one and it downloads on demand. Two side effects are worth knowing while you settle in: everything in these folders now counts against your iCloud storage quota, so a video-heavy Desktop can fill a small plan in one afternoon; and on a slow connection the initial upload can run for hours, during which files are perfectly usable locally — the progress wheel next to the folder name in Finder tells you where things stand.

The second-Mac wrinkle: a folder named after your computer

Turn the same setting on for a second Mac and Apple has a merge problem: two different Desktops can't both be "the" Desktop. Its solution: the second Mac's files land in a subfolder named after that machine — you'll find Desktop – MacBook Air (or similar) inside the iCloud Desktop folder. Nothing is combined automatically. If you want one unified Desktop, drag the contents of the machine-named folder out into the main one, resolve any name clashes yourself, then delete the empty folder.

Getting files back to a local, non-synced Desktop

If you didn't want this feature, reverse it in the right order — the toggle-off behaviour surprises people more than the toggle-on:

1. First copy everything somewhere local. In Finder, open iCloud Drive's Desktop and Documents folders, select all, and drag to a temporary local folder (e.g. one you make in your home folder). Option-drag copies instead of moving. Make sure any cloud-icon files finish downloading — right-click → Download Now.
2. Open System Settings → your name → iCloud → iCloud Drive (on Sequoia, under Saved to iCloud) and turn off Desktop & Documents Folders.
3. Your local ~/Desktop and ~/Documents come back — empty. That's the surprise: macOS leaves the files in iCloud Drive (in folders now shown as "Desktop" and "Documents" under iCloud Drive) rather than moving them home for you.
4. Move your files from the temporary folder (or straight from those iCloud Drive folders) back into the real Desktop and Documents, then delete the iCloud copies if you no longer want them in the cloud.

Deciding whether to keep it

The feature is genuinely useful if you work across two Macs — same Desktop everywhere, and a lost laptop costs you nothing. It's a poor fit if your Desktop hosts huge video projects (uploads forever, eats iCloud quota) or if you need files guaranteed present with no internet. If quota is the objection, fix that instead of the feature: prune what's syncing or step up a tier.