The Obsidian-versus-Logseq preference is Jonker's opinion. The product facts below come from Logseq's own announcement, its community FAQ, its GitHub README and Obsidian's documentation.
What Logseq actually changed
Logseq's team announced the split on April 24, 2026. Obsidian's Bases feature, by contrast, is described as an editor and visualization layer over the YAML frontmatter in your Markdown files. I'll come back to that. First, Logseq's side.
Per the announcement, the two products are:
- Logseq OG is the file-based, Markdown product. It is meant for people who prefer local Markdown files and has a new repository.
- Logseq is the database-graph product. It stays in the existing repository and is aimed at sync, collaboration and performance.
The team said nothing changes immediately for people with Markdown graphs. It also said nobody is forced to migrate, and that OG will get security and Electron upgrades but no new features. Both apps can be installed side by side, with file graphs in OG and database graphs in the new Logseq.
The unofficial community FAQ, written by volunteers, explains the key technical difference. Both versions use an in-memory database while the app runs. In the OG version the Markdown files on disk are the canonical copy. In the new version the canonical copy is a SQLite database, and you can export Markdown but cannot change your graph by editing files directly. The FAQ says the tradeoff is meant to buy better sync, real-time collaboration and less data loss.
Markdown Mirror: close, but not the same
The headline claim "Markdown is gone" needs a qualifier. Logseq's database version has a Markdown Mirror feature, and the roadmap in the announcement lists it among work in progress. A community development update, as relayed in the research brief, describes it as an opt-in projection of your graph to a folder that updates as the database changes. You can search the mirrored files with tools like grep or ripgrep, put them in Git, or open them in another editor.
Edits to those files do not flow back into Logseq. Two-way editing was still in development in the update I was given. I couldn't open that forum post myself, so I'm relying on the research brief's account of it. The FAQ is consistent with this, describing the idea as one-way and not committed to.
Here is what that means in practice:
| Workflow | Logseq OG (files) | Logseq (database) |
|---|---|---|
| Edit notes in another editor | Yes | No, not into the graph |
| Read-only searching or archiving of Markdown | Yes | Via export or Mirror |
| Sync via Git or Syncthing | Yes, the FAQ suggests these for OG users | Use Logseq's own sync, including a self-hosted option |
| Canonical copy | Markdown files | SQLite database |
The beta warning
The Logseq README says the database version is in beta, with the mobile app and real-time collaboration in alpha. It states plainly that data loss is possible. It recommends automated backups or regular SQLite backups, plus a dedicated test graph and a non-critical project. The FAQ adds that importing a Markdown graph doesn't touch your original files, and it suggests experimenting with a fresh database graph before importing old notes.
Jonker calls the warning fair for a new release, and that seems right. Even so, it is a different promise from "your notes are just files you can open anywhere."
Why Obsidian's approach differs
Obsidian's Bases arrived in version 1.9.0. Its changelog says all the data in a base is backed by your local Markdown files and properties stored in YAML, and the .base file format and syntax were introduced to support it.
Obsidian's help documentation says note properties are only available for Markdown files and are stored in the YAML frontmatter of each note. It also describes formula properties as defined in the .base file itself. In short, the structure sits on top of the files. It doesn't replace them.
Some other facts the comparison rests on:
- Obsidian's own documentation lists table, list, cards and map views, and its syntax page shows a kanban-style view example too.
- Obsidian's February 2025 announcement made its Commercial license optional. It said your data remains stored locally in plain text Markdown files, with no account, ads or tracking. That is the policy statement; the announcement doesn't cover later pricing details.
- The JSON Canvas specification is version 1.0, dated March 11, 2024. It defines a JSON format built from nodes and edges, and the repository's resources are MIT-licensed.
Jonker also credits Steph Ango's "File over app" essay for Obsidian's philosophy. I haven't independently checked that essay, so treat that as his attribution.
Fair counterpoints
Choosing files over a database isn't automatically the right call:
- Logseq's team argues that maintaining two architectures in one app slowed everything down. It says the database enables real-time collaboration, scalable graphs, encrypted sync and a developer platform.
- Obsidian's Bases doesn't match everything the database model offers. Jonker concedes this himself.
- Obsidian is not purely file-only. Its optional paid Sync and Publish services exist, and the dollar figures in the XDA article's spec box are the author's, not something I verified.
- Logseq OG remains a supported file-based option for now, but the team's own FAQ says the long-term future of official OG sync is uncertain.
What Windows users should do
- Identify which app you have. Logseq OG and the new Logseq are separate apps. Don't assume file-editing workflows apply to the database one.
- Back up before experimenting. Copy your vault or graph folder first. If you try the database beta, use a dedicated test graph.
- Don't rely on the mirror as an editable source. Treat it as a read-only copy for search, Git or archiving.
- Check your sync setup. Git, Syncthing or cloud-folder sync works naturally with file graphs. The database version expects its own sync.
- Test your exit. Try opening a sample of your notes in a plain text editor. If they come out readable, you have the portability the XDA piece values.
Bottom line
The file-versus-database split is a real architectural choice, not just a rebrand. Logseq's database version is a beta that trades direct file editing for sync and collaboration features. Obsidian adds database-style views while keeping Markdown as the canonical store. Which one suits you depends on whether you value editable files or the new collaboration features more.