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
21% 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.
HackMD — Available as a hosted service or via its open-source community edition, it offers a Google Docs-style real-time multi-user editing environment with built-in GitHub synchronization so your actual files stay as standard Markdown.
Visual Studio Code + Live Share — By using VS Code with standard .md files and the Live Share extension, you get real-time collaborative editing over local files stored directly on your machine or in a Git repository.
Outline — An open-source, team-based knowledge base and wiki that backs everything with standard Markdown and structural organization, designed explicitly for team collaboration without trapping your data.[](https://www.markdownguide.org/tools/)
Would you prefer a self-hosted web application (like HedgeDoc) or an editor extension/plugin setup that works with local files on your computer?
If your priorities are real-time collaboration, native Markdown, and freedom from proprietary document formats, I'd start with HedgeDoc and HackMD. Both are built around Markdown rather than treating it as an export format, but they differ in how much control you want over hosting and your data.
Best collaborative Markdown editors
1. HedgeDoc
(Best for ownership)
An open-source, self-hostable editor with real-time collaboration, revision history, sharing controls, and Markdown-based notes. You can run it on your own server and export notes as .md files.
Trade-off: You manage the hosting if you want full infrastructure control.
A hosted collaborative Markdown workspace with live editing, comments, mentions, version history, and GitHub integration. Its documentation describes Markdown as the underlying authored and stored format, with Markdown access through its API and CLI.
Trade-off: It's a hosted service, so you depend on its platform for the collaborative experience.
A particularly interesting option if you already keep documents in ordinary folders, an Obsidian vault, or a Git repository. It aims to add real-time collaborative editing while leaving your Markdown files on disk as the source of truth.
Trade-off: It's a more developer-oriented option; check its setup requirements and maturity before adopting it for a whole team.
My recommendation is HedgeDoc if you want a straightforward collaborative editor without giving up control. If your documents must remain ordinary .md files in an existing repository, investigate CollabMD first.
One important distinction: Markdown portability isn't the same as complete portability. Before committing, test exporting a document containing tables, images, diagrams, and comments. Comments, revision history, permissions, and uploaded assets may not all travel with the Markdown file.
One question that would help me narrow this down: Do you want a hosted service that works immediately, or are you happy to self-host it or store everything in Git?
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 you want a note-taking app with bi-directional linking and Markdown, I'd start with Obsidian. It's particularly good if you want to build a personal knowledge base where notes link to one another and you can see which other notes reference each idea.
Here are the best options, depending on how you like to take notes.
Top note-taking apps to consider
1. Obsidian
(Best overall)
Stores notes as local Markdown files, supports backlinks and internal links, and offers a graph view of your connected notes. You can keep your files and choose how to sync them.
Best for: Long-term knowledge management, research, journaling, and personal wikis.
Website:
2. Logseq
Designed around linked notes and an outline-style workflow. It supports backlinks, page links, block references, and Markdown.
Best for: Daily notes, meeting notes, research, and connecting individual bullet points across documents.
Website:
3. Joplin
A strong option if you prefer a traditional notebook-and-folders structure with Markdown editing and open-source software. Its linking workflow is less centered on a connected knowledge graph than Obsidian's.
Best for: Organized notes, clipping web pages, and a more conventional notebook experience.
Website:
4. Anytype
A more visual, object-based approach to organizing and connecting information. Worth considering if you like structured pages and relationships, though it is not as straightforward a plain-Markdown file workflow as Obsidian.
Best for: Visual organization, connected information, and customizable personal workspaces.
Website:
Quick comparison
App
Bi-directional links
Markdown
Main advantage
Obsidian
Built in
Native files
Flexible, powerful knowledge base
Logseq
Built in
Supported
Excellent block-level linking
Joplin's core Markdown workflow is documented officially, and its plugin directory includes tools for backlinks and bidirectional links.
My recommendation
Choose Obsidian if you want the simplest combination of Markdown files, backlinks, cross-linked notes, and long-term portability.
Choose Logseq if you think in outlines, daily journals, and individual blocks of information rather than longer documents.
One question that would help narrow it down: what devices will you use it on?
Building a "second brain" doesn't mean you need a massive, complicated system. In fact, starting too complex is the #1 reason people give up.
Depending on how your mind works, here are the simplest and most effective tools to get started:
Obsidian : Great if you value privacy and longevity. It stores everything as plain text files right on your computer (no cloud lock-in) and uses simple double-bracket syntax ([[note name]] ) to link ideas together. It has a bit of a learning curve visually, but structurally it’s as simple as a folder of text files.[](https://tana.inc/blog/best-second-brain-apps-2026)
Notion : Great if you like visual structure, tables, and databases. It is heavily customizable, meaning you can build a gorgeous dashboard, though it's easy to fall into the trap of spending more time designing your workspace than actually taking notes. You can check out structured setups like the Notion Second Brain Template if you want a head start.[](https://tana.inc/blog/best-second-brain-apps-2026)
Logseq : Great if you think in bullet points and outlines. It centers around a daily journal page where you just dump your thoughts, and you can easily link or nest concepts without worrying about rigid folder hierarchies.[](https://tana.inc/blog/best-second-brain-apps-2026)
Apple Notes or Google Keep : Don’t overlook the basics. If you just want to capture things instantly on your phone without installing specialized software, a single "Inbox" folder in a default notes app is the lowest-friction place to start.
To see how a streamlined, markdown-based workflow looks in practice, you can watch this overview on Best second brain apps to see a quick workflow in action.
To help narrow down the best fit, tell me:
Do you prefer writing in free-form pages or bullet-point lists?
Do you want your notes stored locally on your device or in the cloud?
If you want to build a “second brain” for your thoughts, ideas, notes, and things you want to remember, my advice is to start with a simple tool rather than spend weeks building the perfect system.
My top recommendation is Obsidian if you want to connect ideas over time, or Notion if you want an organized workspace for notes, goals, and projects. Both are popular choices for personal knowledge management.
Three simple tools worth considering
1. Obsidian
(Best for connecting ideas)
Keep notes, personal insights, research, and ideas connected through links between notes. Your notes are stored as local plain-text Markdown files.
I need to organize my notes and ideas. How can I create a personal knowledge management system?
Can you guide me through the process of creating a personal knowledge management system?
Which note-taking app, Notion or Obsidian, is better for creating a personal knowledge management system for a technical user?
How do I set up a system for personal knowledge management?
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.
Joplin : Best open-source Evernote/Obsidian alternative if you want a more traditional hierarchical folder layout combined with Markdown and an optional web clipper. While its bi-directional linking isn't as heavily emphasized as Obsidian's or Logseq's, it supports internal note links cleanly.[](https://www.tinystartups.com/blog/best-markdown-note-taking-apps)
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)?
