How to sync markdown notes across devices (and keep them private)

The problem

A folder of markdown files is the most durable note system there is. It is also stubbornly single-machine, and the moment you want the same notes on a laptop, a desktop, and a phone, you need to pick a sync mechanism. They are not equal, and the differences are mostly about two things: conflicts and privacy.

Here are the five approaches that actually work, honestly assessed.

1. A cloud drive folder (iCloud, Dropbox, Google Drive)

Put the notes folder inside the drive folder and you are done.

• Good: free, zero setup, works with any editor.
• Bad: the provider reads your files. Plain markdown means plainly readable notes on someone else’s server, scanned and indexed under whatever policy applies this year.
• Ugly: conflicts. Edit the same note on two devices before they catch up and you get a duplicate “conflicted copy” file, silently, next to the original. Mobile support for arbitrary folders is patchy, especially on iCloud outside Apple’s apps.

Fine for low-stakes notes you only edit on one device at a time.

2. Syncthing

Peer-to-peer folder sync between your own devices. No server holds your files at all.

• Good: genuinely private, free, open source, fast on a home network.
• Bad: devices only sync when both are on, so a note written on the desktop is not on your phone unless the desktop is still running. Setup is technical. Conflict handling produces .sync-conflict files you clean up by hand.

The best free option for technical users with always-on hardware.

3. Git

Commit your notes and push to a private repository.

• Good: full history, real merges, free.
• Bad: it is a workflow, not a sync. You commit, pull, and resolve conflicts yourself, and doing that from a phone ranges from painful to impossible. Private repos also sit readable on the host’s servers.

Great for developers who already live in git and mostly write at a keyboard.

4. Obsidian Sync

If you use Obsidian, its first-party sync is solid: end-to-end encrypted, automatic, with version history.

• Good: encrypted, reliable, works on iPhone.
• Bad: $4 to $8 a month, tied to Obsidian, syncs only your own devices, and history is capped at one month on the standard plan.

5. Jotura Sync

Jotura is a local-first markdown app, and its sync was designed for exactly this problem. Notes are encrypted on your device before they leave, so the server never sees your words, titles, or folder names. Edits from two devices merge automatically instead of spawning conflict copies. Every synced note keeps three years of version history.

• Good: end-to-end encrypted, automatic and conflict-free, desktop and Android, includes sharing folders or notes with other people, which none of the options above can do encrypted.
• Bad: £4 a month, and it syncs through Jotura’s server (as ciphertext), so if peer-to-peer is a hard requirement, Syncthing is your answer. No iPhone app yet.

Your files stay plain markdown in an ordinary folder throughout, so trying it commits you to nothing: the folder outlives any app you point at it, this one included.

The short version

You are	Use
Non-technical, low-stakes notes	A cloud drive folder
Technical, own always-on hardware, want free	Syncthing
A developer who writes at a keyboard	Git
An Obsidian user on iPhone	Obsidian Sync
Anyone who wants encrypted, automatic, shareable sync	Jotura Sync