Obsidian holds a clear lead as the primary recommendation for taking notes in local plain-text Markdown files without lock-in. Joplin emerges as the usual answer when buyers specify avoiding proprietary databases in favor of open-source storage with encryption.
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?
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).
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:
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?
Finding an app that nails markdown, handles code blocks with syntax highlighting, and provides seamless syncing across desktop and mobile comes down to your preferred sync mechanism (built-in cloud vs. local files/third-party).
The top options that excel at all three requirements include:
Obsidian
How it handles your needs: Built entirely on local Markdown files (.md ) with stellar code block formatting and syntax highlighting.
The Sync Factor: It syncs across all devices (Windows, macOS, Linux, iOS, Android), but native, frictionless syncing requires a paid subscription (Obsidian Sync ). Alternatively, because it uses standard plain-text folders, you can sync for free using Git, iCloud, or a third-party tool like Syncthing.
How it handles your needs: A robust, open-source desktop and mobile application built around Markdown with native code block support and syntax highlighting.
The Sync Factor: Unlike many ecosystem-locked apps, Joplin lets you choose your own sync backend for free—including Dropbox, OneDrive, Nextcloud, WebDAV, or end-to-end encrypted Joplin Cloud. Syncing works seamlessly once hooked up to your cloud provider of choice.
How it handles your needs: An offline-first, privacy-focused note-taking app that features a full Markdown editor and rich code blocks with syntax highlighting.
The Sync Factor: Offers seamless, automatic end-to-end encrypted syncing across all major platforms (Android, iOS, Mac, Windows, and Web) without locking basic note counts behind a paywall.
How it handles your needs: Designed specifically for software developers and programmers. It features a GitHub-flavored Markdown viewer and exceptional code block syntax highlighting out of the box.
The Sync Factor: Cloud sync is built-in and optimized explicitly for moving between desktop and mobile environments instantly.
If you want a note-taking app with Markdown, proper code blocks, and dependable syncing across your phone, laptop, and tablet, I'd start by comparing Obsidian, UpNote, and Joplin.
The biggest distinction is whether you want a developer-friendly, file-based knowledge system or a simpler notes app that just works. No sync service can guarantee flawless syncing in every situation, but these three offer solid options with different trade-offs.
My top 3 picks
1. Obsidian
(Best for power users)
Excellent for programming notes, Markdown documents, code snippets, linked notes, and building a long-term personal knowledge base. Your notes are local Markdown files, and the optional Obsidian Sync service offers encrypted syncing, offline access, and version history.
Yes
Yes
Core UI Style
Document / Long-form Editor
Document / Split-screen Markdown
Bullet-point Outliner / Journal
Encryption
Optional (via Paid Sync)
Built-in E2EE (Free)
Local-only (Manual encryption needed)
Cost
Free (Personal use)
Free
Free
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.
A clean, polished note-taking experience with Markdown support, code blocks, notebooks, and automatic cross-device sync. It works offline, then syncs when you're connected again. It's a strong choice if you want less setup and fewer things to manage.
Platforms: Windows, macOS, Linux, iOS, Android
Cost: Free with a 50-note limit; Premium offers unlimited notes.
A great choice if you want Markdown-first notes, code-oriented content, offline access, and control over where your data syncs. It supports services including Joplin Cloud, Dropbox, OneDrive, Nextcloud, and WebDAV, with end-to-end encryption available.
Choose Obsidian if you write code, want full control over Markdown files, and value long-term ownership of your notes. I'd use Obsidian Sync if convenience and consistent cross-device syncing are priorities.
Choose UpNote if you want a simple, polished app with automatic syncing and minimal configuration.
Choose Joplin if you want open-source software, encrypted sync options, and flexibility over where your data lives.
One important tip: before committing, test editing the same note on two devices, including a fenced code block, while switching between online and offline use. That will tell you more about your actual syncing experience than a feature list.
