Obsidian holds a wide lead across note-taking tools, frequently cited for local Markdown storage, bi-directional linking, and personal knowledge management. When users need subscription-free handwriting support across devices, Microsoft OneNote becomes the usual answer.
Since July, Gollumrising has become the go-to answer for flat-file Markdown team wikis, with LeafWikirising and WikiMDrising joining the most named options. Colibrirising has become a common answer for collaborative Markdown document editing.
Latest insights
Week of Sep 21–27 · Since Jul 5
Joplin Gaining: Joplin now ranks #5 in Note-Taking Apps & Wikis, up from #6
Joplin Gaining: Joplin moved ahead of Logseq in Note-Taking Apps & Wikis
Joplin Gap between platforms: Joplin's platform gap in Note-Taking Apps & Wikis widened: ChatGPT Search 26.7%, Google AI Mode 15.6%
Logseq Gap between platforms: Google AI Mode now mentions Logseq 11.1 points more often than ChatGPT Search in Note-Taking Apps & Wikis, a narrowed gap
Logseq Slipping: Logseq now ranks #6 in Note-Taking Apps & Wikis, down from #5
20% of citations point at the ranked brands’ own sites. reddit.com, youtube.com, github.com are the most-cited sites outside the ranked brands’ own domains.
If your priority is real-time collaboration + Markdown as the actual document format, rather than exporting from a proprietary editor, these are strong options:
hedgedoc.org — Probably the cleanest fit. It is open source, self-hostable, and built specifically around collaborative Markdown. Multiple people can edit simultaneously, with live preview.
hackmd.io — A polished hosted collaborative Markdown editor. Its current product documentation says Markdown is authored, stored, versioned, and served as Markdown rather than merely being an export format.
.app — Particularly interesting if you already have a folder of files. It works directly with local Markdown files, supports real-time collaboration, and is open source/self-hostable.
I need a note-taking app that supports handwriting and does not charge a subscription for syncing.
I need a team wiki that stores data as markdown files and does not use a proprietary database.
What is the best note-taking app?
collabmd
.md
usemdocs.com — A newer option built around plain Markdown, with Google-Docs-style multiplayer editing plus a Git-like CLI workflow. It explicitly describes Markdown as the lossless source of truth.
getoutline.com — More of a collaborative knowledge base than a pure Markdown editor, but it supports real-time collaboration and Markdown export/copy. Its documents aren't exclusively stored as .md files, so it's a weaker fit if avoiding proprietary storage is your central requirement.
My practical shortlist
If you want…
Consider
Self-hosted, mature Markdown collaboration
HedgeDoc
Best polished hosted experience
HackMD
Edit an existing Markdown folder directly
CollabMD
Markdown + Git/CLI workflow
mdocs
Wiki/knowledge-base features alongside Markdown
Outline
If by “does not lock me into a proprietary format” you mean “I want the canonical files to remain ordinary .md files on my filesystem/Git repo”, I'd narrow the field to CollabMD, mdocs, and HedgeDoc, with the first two especially aligned with that requirement.
Would you prefer a browser-based tool you can self-host (like HedgeDoc via Docker), or are you looking for something that integrates into a local folder/Git workflow?
Yes. My top recommendation is MkDocs if your priority is keeping documentation in a genuinely open, portable format.
🥇 MkDocs — best fit
MkDocs stores your source documentation as ordinary .md files in a directory, typically alongside a small mkdocs.yml configuration file. It generates a static website from those files.
Why I like it for a team:
Markdown files are the source of truth — no proprietary database or document format.
Works naturally with Git/GitHub/GitLab, so changes can go through pull requests and version history.
The resulting site is static HTML, so you can host it essentially anywhere.
Open-source, BSD-2-Clause licensed.
Lots of themes/plugins, including the popular Material for MkDocs ecosystem.
🥈 Docusaurus — better for a polished documentation portal
Docusaurus is another excellent choice. It uses Markdown/MDX files, supports hierarchical docs, versioning, localization, search integrations, and generates a static site.
The tradeoff is that Docusaurus is more of a documentation website framework than a simple team wiki. It also uses MDX, which adds capabilities beyond standard Markdown.
For most engineering/product teams, I'd start with MkDocs + Git. Your actual knowledge remains a folder of Markdown files, meaning you can move to another renderer—or simply read/edit the files directly—without having to migrate out of a proprietary database.
If you tell me whether your team is technical or non-technical, I can also recommend a few open-source wiki tools with a browser editor that still keep the underlying content portable.
If bi-directional linking + Markdown are your two must-haves, I’d shortlist these:
Obsidian — Probably the closest match. Notes are stored as local Markdown files, and [[wikilinks]] automatically create relationships/backlinks between notes. It also has graph view, block-level links, and a large plugin ecosystem.
Logseq — Great if you like outlining and daily journals. It supports Markdown files, linked references, block references, and queries, with a more outliner-oriented workflow than Obsidian.
Zettlr — Worth considering if your notes are heavily research/academic oriented. It works directly with Markdown files and is designed around linked knowledge and writing workflows.
My practical recommendation
Start with Obsidian if you want a flexible, general-purpose personal knowledge base. Its combination of real .md files + backlinks + graph view + extensibility is unusually strong.
If you tell me whether you're on Windows, Mac, iPhone, Android, or Linux, and whether you need sync/collaboration, I can narrow it down to 2–3 options.
Here are the top note-taking applications that combine powerful bi-directional linking with native Markdown support, each tailored to slightly different workflows:
— An open-source, privacy-first outliner that stores your notes locally as Markdown or Org-mode files. It centers around a daily journal workflow with robust block-level bi-directional linking, built-in PDF annotations, and flashcards. You can check it out at the .[](]()]()
I'm looking for a Markdown-based note app that features bi-directional linking. Can you recommend any?
Building a "second brain" (inspired by Tiago Forte’s methodology) doesn't require an overly complex setup. The key is finding a clean, low-friction tool that lets you capture, organize, and retrieve notes easily.
Here are some of the simplest and most effective tools for a second brain:
Obsidian: A markdown-based app that stores notes locally on your device. It’s lightning-fast, highly customizable, and uses bi-directional linking to map how your thoughts connect without forcing you into a rigid hierarchy. Check out the Obsidian Official Website to get started.
Notion: A flexible, all-in-one workspace that lets you build databases, kanban boards, and nested pages. It has a bit more of a learning curve than Obsidian, but it’s great if you prefer a visually rich, dashboard-style setup. You can explore features on the Notion Website.
Logseq: An open-source, privacy-first outline-based platform. It is heavily focused on daily journaling, flashcards, and graph-based linking, making it brilliant for rapid capturing of daily thoughts. Learn more at the Logseq Website.
Apple Notes: Surprisingly capable for a minimalist approach. With recent updates supporting folder structures, tags, and quick-note features, it is already on your Apple device and offers zero friction for capturing ideas on the go.
Google Keep: The ultimate tool for ultra-fast, lightweight capture. It's best suited for quick checklists, snippets, and fleeting thoughts rather than deep, interconnected knowledge management.
Would you like to narrow this down? Tell me:
What device/operating system you primarily use (Mac, Windows, iOS, Android)?
Whether you prefer a folder structure or a networked/linked note style?
I can help you choose the best fit for your workflow.
If you want something simple that can grow into a real “second brain,” I’d start with Obsidian.
obsidian.md is essentially a folder of Markdown notes with easy links between ideas. Your notes stay on your device, and you can connect related thoughts with [[links]], tags, and backlinks.
A very simple setup
Create just these four areas:
Inbox — random thoughts, ideas, things you don't want to forget
Projects — things you're actively working on
Areas — ongoing parts of life/work
Ideas & Notes — things you've learned or want to explore
Then follow one rule:
Capture first. Organize later.
For example, you might write:
# Idea: Personal knowledge dashboard
I want one place where I can see what I'm learning.
Related:
[[Note-taking]]
[[AI]]
[[Personal productivity]]
Over time, those links create a network of ideas rather than a giant hierarchy of folders. Obsidian also has a graph view and Canvas for visually exploring connections.
The nice part is that you don't need to build an elaborate “second brain” system on day one. Start with one folder and one daily note. Obsidian is free for the core app, and its mobile apps are available on iOS and Android.
If you want, I can also give you a dead-simple 5-minute Obsidian second-brain setup with the exact folders, templates, and rules to use.
If your priority is owning your notes as ordinary files that you can open, back up, edit, and move to another app at any time, look for a local-first note-taking app that stores notes as Markdown (.md) or plain text (.txt) files on your own device.
I'd start with these three options. They offer a good balance of portability, usability, and freedom from proprietary data formats.
My top recommendations
1. Obsidian
(Best overall)
Your notes live as ordinary Markdown files in a folder you control. It has excellent linking between notes, search, backlinks, graph visualization, and a large plugin ecosystem.
Trade-off: Obsidian itself is proprietary, even though your notes are portable and readable without it.
Best for: a personal knowledge base that can grow for years.
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.
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.
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.
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.
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.
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
If you want…
Choose
The best all-around experience
Obsidian
Open-source software and local files
Zettlr
Daily journaling and linked bullet points
Logseq
Mobile apps, attachments, and flexible sync
Joplin
The least possible lock-in
Plain Markdown files
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?
The most reliable, highly-regarded apps built specifically around a plain-text, non-proprietary format include:
Obsidian is the gold standard for plain-text note-taking. It acts as an overlay on top of a local folder (called a "vault") filled with standard Markdown files.[]()
Which note-taking apps avoid proprietary formats and just save my notes as simple text files?
I need a cross-platform note app that doesn't lock me into a specific format. It must support handwriting, Markdown, and code blocks.
I need a note-taking app that supports Markdown and does not store notes in a proprietary database.
If you want complete ownership of your data, you are looking for local-first, plain-text Markdown editors . These apps store your notes directly as standard .md files in regular folders on your hard drive, meaning you can open, edit, or back them up using any text editor or file manager without ever being locked into a proprietary format.
Here are the best options available depending on your exact workflow:
Obsidian is probably the closest match. It uses real Markdown files, supports fenced code blocks, works on Windows/macOS/Linux/iOS/Android, and its first-party Sync works across devices with offline support and version history.
Etherpad with the ep_markdown plugin is a classic, ultra-fast real-time collaborative text editor. While standard Etherpad is purely operational-transformation plain text, adding the Markdown plugin allows you to view, import, and export your collaborative pads directly as Markdown. It is entirely open-source with zero proprietary formats, though its live editing is WYSIWYG/stylistic rather than "type-the-syntax-as-you-go".[](https://github.com/ether/ep_markdown)
SilverBullet is a newer, open-source, local-first and self-hosted collaborative space. It treats your entire workspace as a collection of plain Markdown files stored right on a server or your local machine, allowing real-time sync and page editing across clients without locking you into a proprietary cloud or database structure.
Zettlr — An open-source Markdown editor specifically built for researchers, journalists, and academics. It combines deep bi-directional linking and Zettelkasten method features with seamless citation management and export tools. Learn more via the Zettlr Official Website.
AppFlowy — An open-source, local-first alternative to Notion that lets you control your data. It supports Markdown and connected databases, making it a strong choice if you prefer structured relational views alongside your linked notes. You can explore the project on the AppFlowy Official Website.
Foam — A personal knowledge management system built as an extension for Visual Studio Code. It turns VS Code into a bi-directional linking workspace using Markdown, making it an ideal option if you already live inside a code editor. Details are available on the Foam VS Code Extension Page.
To help narrow down the best fit, tell me:
Do you prefer a traditional document/folder structure (like Obsidian) or a bullet-point outliner (like Logseq)?
Do you need local-first privacy or cloud-synced collaboration out of the box?
Obsidian is probably the closest match to what you're describing. Your notes are ordinary Markdown files in a folder you control, while Obsidian adds wiki-style [[links]], backlinks, graph visualization, properties, search, and a huge plugin ecosystem.
One particularly nice feature is that backlinks aren't merely a graph visualization: Obsidian can show both linked references and unlinked mentions for the current note.
It also supports regular Markdown links if interoperability is more important to you than Obsidian's [[wikilink]] syntax.
🥈 Logseq if you think in outlines
Logseq is my pick if your notes naturally look like nested bullet points and daily journals. Its distinctive advantage is block-level linking and references, so you can connect individual thoughts rather than just entire documents.
What I'd choose
Want the safest, most flexible long-term choice → Obsidian
Want a more database/block-oriented system → SiYuan
Doing academic/research writing → Zettlr
Want open source with a more traditional notes workflow → Joplin
If your priority is specifically “I want a folder full of portable .md files that I can still use if I abandon the app”, I'd choose Obsidian. Current comparisons also consistently distinguish it from apps that merely edit like Markdown but store notes in a proprietary database.
If you tell me whether you're on Windows, Mac, Linux, iPhone, or Android, I can narrow this down to the 2–3 best choices for your setup, including sync options and pricing.
Logseq is a privacy-first, open-source outliner that operates directly on top of local plain-text files (supporting both Markdown and Org-mode formats).
Joplin : A fully open-source, offline-first alternative that stores notes locally. While it uses an internal database for indexing performance on desktop, it gives you complete data portability via raw Markdown exports and lets you sync freely using your own end-to-end encrypted storage like Nextcloud, Dropbox, or a local directory. Get it via the Joplin Official Website.
QOwnNotes : A lightweight, native open-source plain-text and Markdown note-taking application designed to work seamlessly with local file directories and optionally integrate with Nextcloud/ownCloud. Your notes are explicitly saved as standard Markdown text files right on your desktop. Explore features on the QOwnNotes Website.
Zettlr : An open-source, highly specialized Markdown editor built specifically for researchers, academics, and writers. It operates strictly out of your local directories, reading and writing native Markdown files while adding robust citation and export tools. Find out more on the Zettlr Official Website.
To help narrow this down, let me know:
What operating systems do you need to sync between (e.g., Windows, macOS, Linux, iOS, Android)?
Do you prefer a traditional folder/file tree or an outliner/daily journal style?
If your requirement is specifically Markdown files on disk, not notes trapped in a proprietary database, there are several good choices.
App
Storage
Open source?
Platforms
Good fit for
Obsidian
Plain .md files in a folder
No
Win/macOS/Linux/iOS/Android
Linked notes, knowledge bases
Zettlr
Plain .md files
Yes
Win/macOS/Linux
Writing, research, citations
Logseq
Markdown/Org files
Yes
Win/macOS/Linux/iOS/Android
Outlining, daily notes, backlinks
MarkText
Plain Markdown files
Yes
Win/macOS/Linux
Simple Markdown editing
Joplin
Internal database, with Markdown import/export
Yes
Win/macOS/Linux/iOS/Android
Traditional notes + syncing
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.
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.
Logseq is another open-source, file-based option, especially if you like an outliner/daily-journal workflow rather than traditional documents.
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.
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.
Here are the top note-taking apps that excel at markdown, gorgeous code blocks, and seamless multi-device syncing, each tailored to a slightly different style:
Obsidian — The Powerhouse for Local Markdown. It stores your notes as a local folder of plain text Markdown files. It features stellar syntax-highlighted code blocks, a massive plugin ecosystem, and blazing-fast performance. Syncing: Free if you use a third-party tool (like Git, iCloud, or Syncthing), or seamless and encrypted via their paid Obsidian Sync add-on.
Notion — The Ultimate Connected Workspace. While it uses a block-based rich text system rather than pure local markdown files, it has incredible markdown shortcut support, industry-leading code blocks with language auto-detection and line numbers, and a stunning UI. Syncing: Flawless cloud sync out-of-the-box across web, desktop, and mobile for free.[](https://www.atlasworkspace.ai/blog/best-cross-platform-note-taking-apps)
Notesnook — The Privacy-First Note Taker. Built with zero-knowledge end-to-end encryption, Notesnook supports full markdown, code blocks, and a clean distraction-free interface. Syncing: Fully cross-platform with built-in instant syncing across all your devices under their account ecosystem.[](https://www.opensourcealternatives.to/blog/best-open-source-note-taking-apps)
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)?
