SiYuan vs Logseq: which open-source PKM app wins in 2026?

Outliner vs block documents — two shapes of thinking

Logseq is an outliner to its core: every line is a bullet, every note is a tree, and the day’s journal page is where everything starts. That shape is superb for interstitial notes, meeting fragments and thinking-in-progress — you indent instead of organizing, and block references let any bullet be quoted anywhere. The cost is that long-form prose always feels like it is being written inside a list, because it is.

SiYuan’s unit is the document: real pages with headings and paragraphs in a WYSIWYG editor, where every paragraph is still an addressable block you can reference and embed. On top sit Notion-style database and attribute views, built-in flashcards and PDF annotation. The same meeting note that lives as nested bullets under today’s journal in Logseq becomes, in SiYuan, a page with headings — and, if you want, a row in a meetings database. Neither shape is more powerful; they match different heads. (If your real comparison is with Markdown files, we’ve compared SiYuan against Obsidian too — and against Anytype, the other privacy-first, self-hostable app.)

Project health in 2026 — the section this audience checks first

Both projects are AGPL-3.0, similarly starred (Logseq 45,500, SiYuan 47,100 on GitHub, read November 7, 2026), and both are shipping. The difference is shipping shape. As of November 2026:

• Logseq spent years rewriting itself around a local database, and the classic Markdown app slowed to three releases in the sixteen months before December 2025. The rewrite landed as Logseq 2.0.1 — the database version — on July 13, 2026, followed by 2.0.2 on October 7, 2026 (a data-integrity release: unsaved edits, undo/redo restoration, mobile sync triggers) and a nightly build on October 25. It is still explicitly beta: the repository recommends automated backups for DB graphs, the new sync is the DB version’s real-time collaboration (RTC) system, and the rebuilt iOS app is in TestFlight with 2.0.2 under App Store review.
• SiYuan ships continuously: v3.8.4 on September 17, v3.8.6 in late September (OAuth 2.1 for its built-in MCP server), v3.8.9 stable on October 29, 2026, and 3.8.10 alpha and beta builds most days into November. No transition, no fork in the road — the app you install today is the one being developed.

Read that as: SiYuan’s health is unambiguous, while Logseq is moving again after a long quiet stretch — but choosing Logseq in 2026 means betting on the database version maturing, or parking on a classic app that is no longer where the attention goes. If you arrived here from the threads this search surfaces — “Leaving Logseq — alternative suggestions?”, “Logseq is different”, a six-year user pushed to SiYuan by a corrupt nightly database — this section is the honest answer to the leaving-Logseq question: the project is alive, and it is still in transition.

Sync and self-hosting

Neither app requires a subscription to be useful, and both can sync without one — with very different amounts of assembly:

• Logseq: classic Markdown graphs sync end-to-end encrypted via Logseq Sync, or free with DIY setups (git, Syncthing, iCloud) since the graph is just files. The database version’s sync is its new real-time collaboration (RTC) system, which the repository describes as the way to sync DB graphs between devices; Open Collective backers ($5/month) get early-access builds, and paid sync pricing for the DB version was not published as of November 7, 2026. There’s no official self-hosted server; self-hosting Logseq means hosting your own file sync.
• SiYuan: a one-time $64 PRO purchase unlocks encrypted sync and backup to your own S3 or WebDAV storage; the official cloud (8 GB) is $148/year. And uniquely in this pair, the entire app self-hosts in Docker — your notes served from your own machine, editable from any browser. For the r/selfhosted crowd, that’s the whole argument.

Looking for SiYuan pricing in full — free tier, PRO, cloud and self-hosting side by side, dated? It lives in our SiYuan vs Anytype comparison rather than being repeated here.

SiYuan vs Logseq with an AI assistant (MCP)

The newer question on this pair is which one Claude, ChatGPT or a coding agent can read and write. SiYuan answers it in the product: its kernel ships a built-in MCP server, authenticated with the workspace API token or — since v3.8.6, September 2026 — OAuth 2.1 so a remote client can sign in, and v3.8.9 (October 29, 2026) added an in-app AI agent with its own tools; the 3.8.10 betas are adding workspace-level long-term memory for it. Logseq has no official MCP server as of the November 7, 2026 read of its repository and releases: the community provides them — servers that talk to the running app’s local API, or, for a classic graph, any filesystem MCP server over the Markdown folder. Most were written for the classic file graph, so check DB-version support before relying on one.

What neither gives you is a boundary. One SiYuan token or grant covers the whole workspace (a request for notebook-level MCP restrictions was closed unimplemented in November 2026), and a Logseq server sees the whole graph. Both are local apps, so the assistant runs on the machine the notes live on, or over a tunnel you set up and secure yourself. If you want a hosted workspace an assistant can reach from anywhere, with a scope you choose per connection, that is a different kind of tool — the Dexi section below and our AI second brain guide cover it.

Performance with large graphs

Logseq’s best-known weakness has been performance at scale: classic Markdown graphs get sluggish as they grow into the thousands of pages — it’s the most consistent complaint in the community, and a large part of why the database rewrite exists. The DB version is much snappier by design, but it carries the beta caveats above.

SiYuan was built database-first from the start — blocks live in SQLite — and it comfortably handles workspaces that would make classic Logseq crawl. Its own trade-off is interface density rather than speed: the app stays fast, but the screen is busy. If you’re arriving with years of notes, this section plus the health snapshot above is most of the decision.

SiYuan review, in brief — what living in it is like

For the Logseq user asking “is SiYuan actually good?”: yes, with a specific texture. It is fast and feature-complete out of the box — you will not spend the first week installing plugins — and the block model, database views and flashcards feel native rather than layered on. The interface is dense: lots of panels, lots of icons, settings that go deep; people coming from Logseq’s spare journal page either enjoy the power or find it busy. Documentation and the plugin bazaar are usable in English but read as translated, and much of the community conversation happens in Chinese. Mobile is functional, not polished. What it never does is feel unmaintained or fragile — and after a long stretch of Logseq waiting, that alone is why some outliner people switch.

Export and lock-in

What’s actually on disk? Classic Logseq: plain Markdown (or Org-mode) files — the cleanest exit in this comparison, copy the folder and leave. The database version moves your graph into SQLite, with export back to Markdown — a fair trade, but the “my notes are just files” era of Logseq ends there. SiYuan stores blocks as JSON in its own local format, and exports documents or whole notebooks to Markdown and PDF; block references and database views flatten on the way out.

Migrating mid-switch: SiYuan imports a classic Logseq graph as Markdown — bullets, text and images come through cleanly, while Logseq-specific syntax travels as literal text: ((block refs)), key:: properties, queries and TODO keywords all need cleanup. The reverse trip (SiYuan → Markdown export → Logseq) works the same way, minus database views. Both directions are an afternoon of link checking, not a one-click move — run a trial import on a copy first.

SiYuan vs Logseq vs Obsidian — where Obsidian fits

The three-way version of this question is the one people type next, so here is the short form. Obsidian is the third shape of thinking: not an outliner, not a block database, but a folder of plain Markdown documents with the largest plugin ecosystem in personal knowledge management — and, unlike both apps on this page, it is closed-source freeware with an open file format rather than AGPL code. Against Logseq it wins on mobile, polish and shipping pace, and loses on outlining and built-in flashcards; against SiYuan it wins on portability and plugins, and loses on built-in databases, self-hosting and licensing. If “my notes are just files” is your first principle, Obsidian beats both; if open source is, it’s out of the running. We’ve done both legs in full: SiYuan vs Obsidian and Logseq vs Obsidian.