The XDA piece on Notion, Obsidian, and Apple Notes losing to a plain folder of markdown files describes a pattern that has been building since the lock-in of cloud notes started biting. When the company hosting your notes changes the pricing model, sunsets the export format, or rebuilds the UI you have spent three years learning, the only file you actually own is the markdown one you can read in Notepad. The apps below all treat a folder of .md files as the canonical store — the app is interchangeable; the notes are not.
We tested the 8 best apps for plain text markdown notes on desktop. The list spans the heavyweight knowledge graphs that earned their reputation honestly, the minimal editors that get out of the way, and the syncing-and-encryption stack for users who want their notes safe on someone else’s server. Every pick reads and writes .md files in a folder you control.
What to look for in a markdown notes app
Pick a markdown notes app that:
- Stores notes as
.mdfiles in a normal folder, not a proprietary database. If the app dies, you should be able to read your notes in any text editor. - Renders standard CommonMark or GitHub-flavoured markdown. Custom dialects are technical debt — your notes should outlive the app that created them.
- Supports backlinks or wiki-style
[[note]]links. Even simple folder-of-notes setups benefit from the connective tissue between related ideas. - Syncs through a method you can verify. Git, iCloud Drive, Dropbox, Syncthing — anything where you can read the raw files on the other end is acceptable.
- Has a working search across the full text. The killer feature of a plain-text note store is that everything is searchable in milliseconds.
Quick comparison
| App | Best for | Platforms | Free plan | Starting price |
|---|---|---|---|---|
| Obsidian | Knowledge graph with plugins | Windows, macOS, Linux | Yes, fully | Free for personal |
| Logseq | Outline-first daily journal | Windows, macOS, Linux | Yes, fully | Free |
| Typora | Live-preview writing | Windows, macOS, Linux | Trial | Around $15 one-time |
| Joplin | Synced encrypted notes | Windows, macOS, Linux | Yes, fully | Free |
| Zettlr | Academic writing with citations | Windows, macOS, Linux | Yes, fully | Free |
| Mark Text | Minimal distraction-free editor | Windows, macOS, Linux | Yes, fully | Free |
| Standard Notes | End-to-end encrypted notes | Windows, macOS, Linux | Yes, basic | Around $30/year |
| Visual Studio Code | Notes inside the editor you already have | Windows, macOS, Linux | Yes, fully | Free |
The 8 best markdown notes apps for desktop
1. Obsidian — best knowledge graph with plugins
Obsidian is the app that pulled the plain-markdown crowd into the mainstream. Notes live as .md files in a vault folder, backlinks build a navigable graph of connected ideas, and the community plugin ecosystem covers everything from calendars to Excalidraw to Git sync. The desktop app is free for personal use; the paid tiers cover commercial use, hosted sync, and publishing — none of which are required to use the editor.
Where it falls short: The plugin culture pulls users toward elaborate setups that distract from actually writing. The mobile app’s sync is paid by default, though you can use Syncthing or iCloud Drive instead.
Platforms: Windows 10/11, macOS, Linux. Mobile apps for iOS and Android.
Bottom line: The default pick for users who want backlinks, plugins, and a folder of markdown files they fully own.
2. Logseq — best outline-first daily journal
Logseq treats notes as outliner blocks first and pages second. The daily journal is the centre of the workflow — every day opens to a new note, and you tag and link from there to build longer-lived pages. Like Obsidian, Logseq stores notes as .md files (or .org for Emacs users), and the graph of links between pages is built from the file content rather than a database.
Where it falls short: The outline-first interaction is divisive — readers who think in paragraphs find it constraining. Performance on very large graphs (10k+ pages) lags behind Obsidian.
Platforms: Windows, macOS, Linux. Open-source under the AGPL.
Bottom line: The right pick when “every day starts with the date and you write down what you did” matches how you actually take notes.
3. Typora — best live-preview writing
Typora is the editor for writing prose rather than building a knowledge base. The interface is one panel with no source/preview split — you type markdown and it renders in place. The result is the closest thing to a Word-like writing experience that still saves clean .md files to disk. Export to PDF, HTML, Word, and a handful of other formats works without fiddling.
Where it falls short: No backlinks or graph view — Typora is an editor, not a knowledge base. The one-time license replaced an earlier free beta and disappointed some long-time users.
Platforms: Windows, macOS, Linux. One-time purchase covers all three.
Bottom line: The right pick when you want to write long-form markdown and stop fighting your editor.
4. Joplin — best synced encrypted notes
Joplin is the open-source notes app for users who want end-to-end-encrypted sync across devices without paying a subscription. Set up the sync target (Nextcloud, WebDAV, Dropbox, OneDrive, or Joplin’s own paid cloud), and notes sync across desktop and mobile with full E2EE if you turn it on. Notes are stored as markdown internally, exportable to a folder of .md files anytime.
Where it falls short: The internal storage is a SQLite database, not a folder of files — you have a folder of .md files only after explicit export. The UI is functional rather than polished.
Platforms: Windows, macOS, Linux. Mobile apps for iOS and Android. Terminal client available.
Bottom line: The right pick when E2EE sync between desktop and phone matters more than a folder of files on disk.
5. Zettlr — best academic writing with citations
Zettlr is built for academic writing. The citation manager integrates with Zotero and BibTeX, the export pipeline handles LaTeX and Pandoc out of the box, and the project view groups long documents into chapters that compile together. Notes are plain markdown files, organised in a folder you point Zettlr at.
Where it falls short: The interface is denser than Typora or Mark Text. Citation setup requires Zotero or a .bib file you maintain yourself.
Platforms: Windows, macOS, Linux. Open-source under the GPL.
Bottom line: The right pick when your notes feed into papers, theses, or articles with citations.
6. Mark Text — best minimal distraction-free editor
Mark Text is what Typora would be if it were free and open-source. Live-preview writing, the same one-panel interaction, basic export to a handful of formats. The feature set is intentionally smaller — no theme marketplace, no plugin ecosystem — and the result is an editor that opens in a second and gets out of your way.
Where it falls short: Development has slowed, with major releases less frequent than the established competitors. Lacks the citation, plugin, and graph features that other tools in this list cover.
Platforms: Windows, macOS, Linux. Open-source under the MIT license.
Bottom line: The right pick for users who want Typora’s writing experience and refuse to pay for it.
7. Standard Notes — best end-to-end encrypted notes
Standard Notes is the notes app where E2EE is the headline feature. Every note is encrypted client-side before it leaves your device, the server only ever sees ciphertext, and the open-source apps are independently auditable. The free tier covers plain-text and basic markdown; the paid tier unlocks editors (rich markdown, code editing, tasks), tags, themes, and longer-term backups.
Where it falls short: The free tier is intentionally limited — you need the subscription for markdown editing and tag organisation. No backlinks or graph view; this is a secure notes app, not a knowledge base.
Platforms: Windows, macOS, Linux. Mobile apps for iOS and Android. Web client available.
Bottom line: The right pick when “no one can read this but me” is a hard requirement and you want a paid product to make that promise auditable.
8. Visual Studio Code — best notes inside the editor you already have
Visual Studio Code is not a notes app, but it is the markdown editor most developers use anyway. Open a folder of .md files, install the Markdown All in One extension, and you have live preview, table-of-contents generation, table editing, and keyboard shortcuts that match the rest of your workflow. Git versioning is one panel away, and remote folder syncing is a normal git push.
Where it falls short: No backlinks or graph view out of the box. The interface optimises for code editing, which is heavy for note-taking. Mobile is essentially not an option.
Platforms: Windows, macOS, Linux.
Bottom line: The right pick for developers who want one editor for everything and are happy to skip the knowledge-base features.
How to pick the right one
Pick Obsidian for the default modern markdown notes experience — a vault folder, backlinks, plugins, and a community that documents every workflow. Pick Logseq instead if you think in outlines and the daily journal is your primary capture surface.
Pick Typora for long-form writing where the editor should stay out of the way, Mark Text for the same experience without paying. Pick Zettlr when your notes feed into academic papers with citations. Pick Joplin when E2EE sync across devices is the headline feature and you can live with notes in a SQLite database internally. Pick Standard Notes when E2EE is non-negotiable and you want the audit trail of a paid product.
Pick Visual Studio Code when you are already in it for coding and your notes are mostly for yourself. Mix freely — every app in this list reads the same .md files, so two of them can point at the same folder and the choice becomes about which editor you happen to have open.
FAQ
What is the best free markdown notes app?
Obsidian is the most fully-featured free markdown notes app for personal use, with vault folders, backlinks, and a large plugin ecosystem. Mark Text is the best free live-preview editor for users who want a clean writing experience without plugins. Joplin is the right free choice when E2EE sync across devices is needed.
Is Obsidian free for personal use?
Yes, Obsidian is free for personal and educational use indefinitely. The paid plans cover commercial use, the hosted Obsidian Sync service, and Obsidian Publish. You can use Obsidian fully featured without subscribing if you do not need those services — Syncthing or iCloud Drive sync your vault folder for free.
Why use plain markdown files instead of a notes app database?
A folder of .md files outlives any single app. You can move to a different editor, search with grep, version with git, and read the files in any text editor on any platform. Notes app databases lock you into the export format the company chooses to support, which has historically been the first thing to break when pricing changes.
Can I sync markdown notes between desktop and phone?
Yes, several ways. Obsidian Sync, iCloud Drive, Google Drive, Dropbox, and OneDrive all sync a folder of .md files between devices. Syncthing is the open-source option that keeps the files on hardware you control. Joplin and Standard Notes sync through their own infrastructure with end-to-end encryption.
What is the difference between Obsidian and Logseq?
Obsidian is page-first — you create pages and link between them. Logseq is outline-first — every note is a tree of bullet points, and the daily journal is the default capture surface. Both store notes as .md files in a folder you control; the difference is the writing interaction.
