Logseq moved my notes out of Markdown files, and that's exactly why I'm sticking with Obsidian

If you used Logseq or Obsidian as your notes app, they always provided a pretty nice safety net when you were trying to pick the right notes app for yourself. They'd just make your notes into raw Markdown files in a folder on your computer, which meant you didn't have to care as much about the notes app you were using. If they ever go away or if the apps get weird, you still have your notes and can access them in pretty much anything.

This year Logseq decided to do something different. They've got this new version out that doesn't exactly treat your notes as files, they now live in a database and Markdown is something you export instead of the thing you're actually writing in. For anyone who picked Logseq because their notes were just files, that's a pretty big change to the original deal. Obsidian has been adding a lot of the same structured, database-style features lately, but it's gone about it without moving anyone's notes out of their folders.

Logseq's notes now live in a database

The app still works as usual, the files just aren't the point anymore

If you're unfamiliar with Logseq, it's a free, open-source note-taking and outliner app that's been around for about six years now. The core part of it is that everything you type is a bullet, and every bullet is its own block you can link to or embed on other pages. If you think in outlines like I do, then you'll probably dig it. However, the Markdown it saved was always a bit odd because block references got written in a syntax no other editor reads, so opening your Logseq pages elsewhere would have probably showed a mess of IDs. And this used to be one of its biggest complaints from users.

In April 2026, Logseq announced it would split into two separate apps. The file-based one got renamed Logseq OG and now only gets security and maintenance updates. Every new feature goes to the new database version, which kept the main name of the app, Logseq. It stores your notes in a local SQLite database instead of a folder of files. That database is the real copy now. You can export Markdown out of it, but you can't open the files and edit them by hand anymore.

Logseq does have something called Markdown Mirror, which writes a plain Markdown copy of your notes to a folder and updates it as you edit. The changes you make to those files don't go back into Logseq yet, though, because the two-way version is still being worked on. Logseq also warns the beta can lose data and tells you to keep regular backups, which I suppose is fair for any new drop. All of this change caused a pretty dramatic rift in the Logseq community, understandably so.

Obsidian was built around the files from day one

Even its own CEO has said the app won't be around forever

Obsidian's whole attitude here goes back to an essay by Steph Ango, who's now the company's CEO. It's called "File over app", and it argues that apps come and go, but the files you make with them have a chance of lasting. He also says outright that Obsidian will become obsolete eventually, and I must say I appreciate this kind of honesty from a CEO.

This thinking is reflected in everything about Obsidian and what it touches, even in areas where Obsidian could have easily made up its own format. For example, Canvas, the app's infinite whiteboard core plugin, saves to a format the team later opened up as JSON Canvas, with a public spec under the MIT license so other apps can read it too. Same thing for properties; anything you attach to a note, like a date or a status, gets saved as YAML at the top of the Markdown file.

If I were to open a note from my vault in a plain text editor, those properties remain completely intact, and moreover, they're actually readable and editable raw. Obsidian has been completely free since February 2025, even if you use it for work, and it makes its money from optional paid extras like Sync and Publish. There aren't any investors behind it either, so there's nothing pushing it towards files getting locked up.

Obsidian gives you database features without the database

It seamlessly does the structure that Logseq rebuilt for

To be fair to Logseq, the reasons behind the database are good ones. Properties in the new version can have proper types, like a date or a number, and queries can pull notes together into dashboard-style pages.

Obsidian ended up doing something similar with Bases, which is a core plugin in version 1.9.0 that turns notes into a database. You can filter notes by their properties and add formulas that work out new values from them, and the results show up as a table or cards, among a couple of other layouts. What makes Obsidian's Bases different is where that data comes from. Everything in a base reads directly from your Markdown files and the YAML properties already in them, and the base itself is saved as a .base file that's also just plain YAML.

This means that when you turn Bases off, it doesn't affect any of your notes. It doesn't cover everything Logseq does. But the whole point is for it to be something simple that sits on top of your existing notes, rather than trapping them in it.

A plain folder is still my favorite feature

Logseq's database version might turn out great, and this isn't about me waiting for its downfall. I wouldn't be shocked if I end up writing about how amazing it turned out to be within a year. But right now, I just want my note stack to be a regular folder, something I could copy to a flash drive and open anywhere else without Obsidian even being involved.