Plain-text Markdown note apps

2. Zettlr

(Best open-source desktop app)

A free, open-source application for working with local text files and Markdown. It supports linked notes, full-text search, tags, and research-oriented writing. It runs on Windows, macOS, and Linux.github.com+1

Trade-off: It's geared more toward writing, research, and organizing documents than toward a polished mobile-first notes experience.

Best for: people who want open-source software and direct control over their files.

Official website ·Source code

3. Logseq

An open-source, local-first knowledge management tool built around daily journals, bullet points, backlinks, and connected ideas. Its website emphasizes local data ownership and Markdown compatibility.logseq.com

Trade-off: Its outliner-style workflow is less like a traditional notebook of documents, and some advanced features may require learning its way of organizing information.

Best for: daily notes, meeting notes, task lists, and interconnected thinking.

Official website ·Source code

Two more worth considering

Joplin

Best if you need desktop and mobile apps, notebooks, attachments, and encrypted sync. It uses Markdown for notes, but its normal storage is app-managed; you can export notes or use filesystem-based synchronization.joplinapp.org+1

Website ·Import/export guide

A plain folder of Markdown files

The most future-proof approach of all. Keep files in folders, edit them in any text editor, and optionally use a Markdown editor for previews and formatting. You can add search, backups, and version history independently.

Best for: maximum simplicity and minimum dependence on any one app.

How I'd choose

One important distinction: open source and open data formats are not the same thing. Obsidian is closed-source but stores notes in ordinary Markdown files. Joplin is open-source but normally manages its notes internally. If you want both open-source software and files directly accessible in a normal folder, Zettlr is a strong starting point.

For the strongest protection against lock-in, use standard Markdown, keep your files in a folder you control, and back that folder up independently. App-specific links, plugins, and metadata can still be less portable than the text itself.

One question to narrow this down: What device will you primarily use?

1. Your main device

Mac or Windows computer

Linux computer

Phone and computer

Phone only

2. Your note-taking style

Simple notes and searchable folders

Linked notes and knowledge base

Daily journal, tasks, and meeting notes

3. Does the app itself need to be open source?

Yes, must be open source

Preferably open source

No, file portability matters more

[Find my best fit]

My shortlist

Obsidian is probably the strongest all-around option. Its official documentation explicitly says notes are Markdown-formatted plain-text files in a folder you control; you can edit them with other editors and manage them with normal filesystem tools.obsidian.md

Zettlr is the one I'd investigate if open source is important too. It works directly with Markdown files and is particularly geared toward long-form/research writing.en.wikipedia.org

Logseq is another open-source, file-based option, especially if you like an outliner/daily-journal workflow rather than traditional documents.github.com

I'd exclude Joplin if "no proprietary database" is a hard requirement. It is open source and Markdown-compatible, but its normal storage model is database-oriented rather than simply being a folder of independently readable .md files.joplinapp.org

If you want the safest long-term format: use an ordinary folder of .md files, with Obsidian, Zettlr, or another editor sitting on top of it. That means your notes remain readable even if the application disappears.

If you tell me your OS (Windows/Mac/Linux/mobile) and whether you need syncing, I can narrow this to 2–3 options and compare their sync, privacy, and backup approaches.

To help narrow this down:

• What operating systems are you syncing between (e.g., Windows, Mac, iOS, Android, Linux)?
• Do you prefer local-first plain text files (like Obsidian) or a cloud-hosted workspace (like Notion)?