Jotura vs Joplin: which Markdown notes app fits you

Both apps store Markdown notes on your own machine, and both are free to install. The first question is where your notes physically live. Joplin keeps them in a local SQLite database and writes Markdown files out when you export. Jotura keeps them as ordinary .md files in an ordinary folder, readable by any editor or script without opening the app.

The second question is licensing and sync cost. Joplin is open source under the AGPL-3.0 license, and it syncs for free through Dropbox, OneDrive, Nextcloud, or WebDAV. Jotura is closed source, the sync it ships costs 4 pounds a month or 40 pounds a year with no free trial, and there is no iOS app. If any of those three is a hard requirement, take Joplin and skip the rest of this page.

Where your notes actually live

Joplin’s storage model is a database: your notes are rows in SQLite, and the app owns them. That buys real things: fast queries, note revision history, and one sync engine that behaves the same on every target. Joplin exports the whole collection to Markdown or to its own JEX archive whenever you want, so nothing is trapped.

Jotura’s storage model is the folder. A vault is a directory of .md files with YAML frontmatter, and that is the whole format. Save a file you did not edit and you get a byte-identical file back, so the app never quietly reformats your Markdown. Jotura opens an existing Obsidian vault as-is, with no import step.

Neither model is better in the abstract. A database wins when you want one app to manage everything. Plain files win when you want other tools and scripts working on the same notes.

Sync compared

Joplin separates the app from the sync target, which is genuinely useful. You pick where your notes go, you can change your mind later, and end-to-end encryption is a switch you turn on for whichever target you chose. Joplin Cloud is the paid option if you would rather not wire up your own.

Basic is 2.99 euros a month and Pro is 5.99 euros a month, both with a 14 day free trial. Check Joplin’s plans page for current figures. Joplin Server is also software you can run on your own hardware, under a noncommercial personal use license. Jotura Sync is hosted by Jotura, with no self-hosted equivalent.

Jotura offers one sync service, and it encrypts everything by default. Jotura derives your keys with Argon2id, a password hashing function, gives every file its own key, and turns file paths into HMAC identifiers so the server never learns your filenames. Setup hands you a BIP39 recovery phrase, the word list format crypto wallets use.

Lose that phrase and you lose the ability to recover the encrypted server copies on a new machine. Your local files are plain Markdown and stay readable either way.

Jotura’s client is closed source, so you are trusting this description rather than reading the code, while Joplin’s encryption is auditable by anyone. If that difference decides it, take Joplin. The security page sets out what Jotura’s server can and cannot see.

Because a Jotura vault is an ordinary folder, you can point Syncthing, iCloud Drive, or git at it yourself. That path is yours to manage, and you give up the built-in merge, the sharing, and the version history.

Joplin gives you more choice and a free path. Jotura gives you one path with encryption that is not optional. It adds encrypted sharing of a folder or a single note, editor and viewer roles, automatic merging of concurrent edits, and three years of version history with attribution. Both people need Jotura Sync for sharing to work.

Feature comparison

	Jotura	Joplin
Source code	Closed	Open source, AGPL-3.0
Notes on disk	Plain .md files	SQLite database, Markdown on export
Platforms	Mac, Windows, Linux, Android	Mac, Windows, Linux, Android, iOS
Free sync	No	Yes, via Dropbox, OneDrive, Nextcloud, WebDAV and others
Paid sync	Jotura Sync, 4 pounds a month, no trial	Joplin Cloud, from 2.99 euros a month, 14 day trial
Self-hosted sync server	No	Yes, Joplin Server
Plugins	None	Yes, an established ecosystem
Web clipper	No	Yes
Publish a note to a public link	No	Yes, on Joplin Cloud
Semantic search	Yes, on device, built in	Not built in, added by community plugins
Agent-oriented command line	Yes: hash-checked writes, memory, agent config sync	Terminal client and REST data API, no agent-specific write safety

Where Joplin wins on features: an iOS app, a plugin system, a web clipper, and publishing a note to a public link from Joplin Cloud. Jotura has none of those. Jotura also has no graph view and no canvas, though neither ships in Joplin either.

What you get in Jotura

Jotura’s editor is what-you-see-is-what-you-get, with a toggle into raw Markdown when you want exact control. Joplin has a rich text editor too. The difference is round-trip fidelity: what Jotura writes back to disk matches what it opened, byte for byte.

Alongside that sit a real table editor, wikilinks with backlinks, daily notes, and a vault-wide task view built from ordinary checklist Markdown. Joplin users reach most of that through plugins, which is a real strength of Joplin. The trade is a plugin you install against a feature that ships.

Keyword search runs over 10,000 notes in about 8 milliseconds in release builds. The core is Rust, running inside Tauri 2. Semantic search, which finds notes by meaning rather than exact words, is optional. Turn it on in desktop Settings and Jotura downloads an embedding model once, then indexes and queries everything on your machine with no API key.

Jotura also ingests documents. Drop in a PDF, a Word file, or a spreadsheet and it creates a searchable Markdown mirror of the contents, so those files turn up in your note searches. Joplin stores the same files as attachments on a note.

The command line and agent angle

This is the clearest split between the two apps. Jotura ships a first-party command line tool called jotura inside the desktop install, built so that scripts and AI coding agents can read and write the vault safely.

HASH=$(jotura read "Projects/Api Rewrite.md" --json | jq -r .hash)
jotura edit "Projects/Api Rewrite.md" --replace "draft" --with "shipped" --if-hash "$HASH"

The --if-hash flag turns the write into a compare-and-set. If the desktop app changed the file after the read, the edit fails instead of overwriting it. Replacements require a unique match unless you say otherwise, every write is atomic, and body edits never touch frontmatter.

jotura memory log --kind decision --title "Chose Postgres over SQLite for the API"
jotura memory recall "database choice"
jotura context "refactor the sync queue"

That memory layer is how an agent keeps decisions between sessions instead of rediscovering them. Agent configuration lives in an Agents/ folder in the vault, and one command writes it out to each tool’s expected location, covering Claude Code, Codex, Gemini, and Copilot.

jotura agents sync

Joplin has its own terminal client and a documented REST data API, and people script against both every day. What it does not have is the write safety an agent needs: hash-checked edits, unique-match replaces, and a memory layer. The CLI reference lists every command.

Moving from Joplin to Jotura

Export with Joplin’s MD - Markdown + Front Matter option. That keeps your tags and your created and updated dates in YAML frontmatter, which is the format Jotura reads. The plain MD - Markdown export drops all of it. Point Jotura at the exported folder and it is a vault.

Two things do not survive the trip. Joplin’s internal note links and its revision history belong to its database, so links may need fixing and history stays in Joplin. Keep your Joplin install until the new vault reads the way you expect.

Which one to pick

Choose Joplin if open source matters to you, or if you need an iOS app. Choose it if you want sync you already pay for elsewhere or host yourself, or if you rely on plugins and the web clipper.

Choose Jotura if you want your notes to be plain files that other tools can read. Choose it if you want encryption on by default rather than as a setting, or if you want a documented command line surface for AI agents working in the same vault.

If neither fits, Obsidian is the other app in this bracket, and that comparison covers it. The Jotura app is free and sync is the only paid part: see download and pricing.