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

Logseq, a free, open-source note-taking and outliner app, recently shifted its approach to storing notes. Instead of keeping notes as raw Markdown files, Logseq now stores them in a local SQLite database. This change, introduced in its latest version, means that users no longer have the convenience of accessing their notes as simple files on their computer.

Obsidian, another popular note-taking app, has been experimenting with similar database-style features recently but has managed to retain the original note files. Obsidian's CEO, Steph Ango, has expressed a philosophy known as "File over app," which emphasizes the longevity of user-created files over the longevity of the apps themselves.

This approach has led to Obsidian becoming completely free since February 2025, made possible by optional paid extras and not relying on investors. The new Logseq database version offers improved property types and query functionality, but it does so at the cost of losing the simplicity and portability of the original file-based app.