Notes Apps That Keep Your Notes as Markdown Files (and Ones That Don't)
Where your notes actually live decides how hard it is to leave an app later. Which popular notes apps store plain Markdown, which lock notes in a cloud workspace, and how to pick.
Most "best notes app" lists rank apps by features. The question that matters more in five years is simpler: where do the notes live? If they are Markdown files in a folder, you can open them in any editor, back them up with any tool and leave whenever you like. If they sit in a vendor's cloud workspace, leaving means an export step that may lose structure.
This guide sorts the popular apps by that one question, then points you to the detailed pages in our directory for pricing and comparisons. Facts come from each vendor's own site and were checked in October 2026. Prices change, so confirm on the vendor page before you buy.
The three storage models
| Model | What it means | Examples |
|---|---|---|
| Plain files on disk | Each note is a .md or .txt file you can see in your file manager |
Obsidian, Typora, iA Writer, Zettlr |
| Local database or open format | Notes are stored locally, usually with an export or sync layer | Joplin, Logseq, Anytype |
| Vendor cloud workspace | Notes live on the vendor's servers in their own page format | Notion, Evernote, OneNote, AppFlowy Cloud |
Bear sits between the first and third: it is an Apple-only app that uses Markdown formatting but keeps notes in its own library rather than loose files.
Plain files on disk
Obsidian keeps notes as ordinary Markdown files in a folder. The app is free for personal use, and Sync costs $4 per user per month billed annually. It is proprietary, which matters if open source is a requirement. See Obsidian alternatives.
Typora is a one-time $14.99 license and shows formatting inline as you type. iA Writer is sold per platform with no subscription. Both are writing tools more than knowledge bases, so they suit drafts, articles and documentation rather than a web of linked notes. Compare them in Typora vs iA Writer.
Zettlr is GPL-3.0 licensed and aimed at academic writing with citations. It is free.
Open formats and local-first
Logseq is open source (AGPL-3.0) and stores local Markdown or Org-mode files, but in an outline format where every line is a block. That is great for daily journals and awkward if you want to open a note as a normal document. Read Obsidian vs Logseq for the trade-offs.
Joplin is open source, lets you choose your own sync service and supports end-to-end encrypted sync. It is the usual answer to "I want something free that I can host myself". See Obsidian vs Joplin.
Anytype is local-first and peer-to-peer. Note that its license is source available, not an OSI open source license, so do not describe it as open source. See Obsidian vs Anytype.
Cloud workspaces
Notion is the dominant choice for teams who want pages, databases and wikis in one place. It imports and exports Markdown, but the native format is blocks, so exports are a conversion. If you are leaving Notion, start with Notion alternatives, and for a self-hostable option read Notion vs AppFlowy.
Evernote and Microsoft OneNote are older, general purpose note apps. Neither is built around Markdown. OneNote is free to use and strong for pen and handwritten notes; Microsoft 365 plans start at $9.99 per month and add Copilot features. Evernote's free plan is limited to 50 notes and one synced device. See Evernote alternatives, OneNote alternatives and Evernote vs OneNote.
How to choose
- You want to own your files. Obsidian if proprietary is fine, Zettlr or Joplin if it is not.
- You write long documents. Typora or iA Writer.
- You think in linked outlines. Logseq.
- You work with a team. Notion or AppFlowy. AppFlowy is the self-hostable choice.
- You live in Microsoft 365 or take handwritten notes. OneNote.
Moving notes between apps
Switching rarely loses text, but it can lose structure. Before you commit to a move, test it with 20 real notes, not an empty vault. Two things break most often: internal links (every app writes them differently) and tables or databases from workspace tools.
Our free tools cover the common conversions without uploading anything:
- Markdown to HTML for publishing notes to a site
- Word to Markdown and PDF to Markdown for importing old documents
- Markdown to Notion when you are moving into Notion
- Markdown table formatter to clean up tables after an export
If you only remember one rule, make it this one: the format your notes are stored in outlasts every feature on the comparison chart.