Skein vs Logseq

Most comparisons of Logseq you will find were written before April 2026 and are now structurally wrong, through no fault of their authors. It is worth getting the current picture straight before comparing anything, because the thing being compared changed underneath.

What happened in April

Logseq announced it was splitting into two products. The database version keeps the name Logseq, and stores your notes in SQLite rather than in Markdown files. The file-based version continues as Logseq OG, and the announcement is candid about what that means: security fixes, dependency upgrades, and a focus on “maintenance and reliability rather than new feature development”.

Both halves of that are worth stating fairly. Logseq has committed in writing that Markdown will always be supported through Logseq OG, and that nobody will be forced to migrate. So “Logseq abandoned Markdown” is not true. But “Logseq keeps your notes as plain Markdown files” is also no longer true without a footnote, and the version carrying the name and the latest release tag is the SQLite one.

The database version also dropped things on the way: whiteboards, slides, the Excalidraw integration, Org-mode support and the built-in Zotero integration, all with the hope that some return as plugins. Flashcards were reimplemented on a new algorithm that does not import the old data. If you are on the file version and considering the upgrade, those are the sentences to read twice.

The table

The real difference, which is not the storage

Logseq is an outliner. Everything is a block in a bulleted tree, and the 2.0 version leans further in by making pages and blocks the same kind of thing. That is not a smaller idea than documents; for some people it is a much better one. If you think in nested bullets, if you write daily journal entries and reference individual lines of them from elsewhere, an outliner fits your head and a document editor will feel like fighting.

Skein is a document editor with links. A note is a page of prose you could have written in any Markdown app, and the connections live between notes rather than between bullets. Block references are on our list under “Later” and honestly labelled as deep work in somebody else’s territory.

So the first question is not which app is better. It is whether you are an outliner person. If you are, Logseq or Roam is your shape and Skein will annoy you.

What Logseq does that Skein does not

• Outlining and block references, properly, as the spine of the app.
• Windows, Linux, iOS. Skein is Mac only.
• Open source, AGPL. You can read it, fork it and run it forever. Skein is free but not open source, and that is a real difference in kind rather than in price.
• PDF annotation, in the app.
• A plugin ecosystem and themes.
• Tags as classes with inherited propertiesin the 2.0 version, which is more structure than Skein’s frontmatter and queries give you.

What Skein does that Logseq does not

• Stays out of the way of your files, permanently. No split, no migration, no database version waiting for you. The file format is the feature and there is no second product where it is not.
• Native, and about a fifteenth of the download. Logseq’s own forum carries long threads about performance on large graphs, including cold starts measured in minutes. Skein’s equivalent problem is real and being worked on in public on the roadmap, on a 5,550-note vault, with the numbers written down.
• A local graph that is a navigator rather than a picture.
• One Markdown engine behind the editor, reading mode and export, with a test that proves the three agree.
• A canvas that did not get removed.Logseq’s whiteboards were dropped in the 2.0 version with the hope of a plugin later. Skein’s canvas is in core, in the open JSON Canvas format.

Who should use which

Use Logseq if you think in outlines, if you want open source, if you need Windows or Linux, or if block references are how you work. It is a serious tool with a serious community.

Use Logseq OG specifically, rather than 2.0, if you are keeping the Markdown files and you have read the maintenance-only sentence and are content with it. That is a reasonable position; it is just one worth taking deliberately.

Use Skein if you are on a Mac, you write in documents rather than bullets, and you want the app under active development to also be the one that keeps your notes as files. Right now that combination is rarer than it was two years ago, which is most of why this post exists.

If your Logseq graph is Markdown, you can point Skein at that same folder today and see how it reads. Nothing is imported and nothing is converted.

Figures checked 14 August 2026, from Logseq’s own announcement, documentation and GitHub release assets (2.0.1, 13 July 2026). Logseq publishes no price list for sync, so none is quoted here. If any of this is out of date, tell me and I will correct it.