SiYuan vs Obsidian: which local-first notes app in 2026?

Markdown files vs a block database — the real difference

Everything else in this comparison follows from one design decision. Obsidian’s vault is a folder of plain .md files: you can open it in any text editor, version it with git, grep it, back it up with anything, and if Obsidian disappeared tomorrow your notes wouldn’t change at all. Links connect files (with heading and block anchors layered on top), and the app is best understood as a very good lens over files you already own.

SiYuan is built the other way around: every paragraph is a block with a permanent ID, stored in SiYuan’s own JSON format with a SQLite index — not as plain Markdown on disk. That’s what makes block-level bidirectional links, block embeds, attribute views and Notion-style databases feel native rather than bolted on: a reference points at a block that keeps its identity when you move or rename things. The trade is legibility — your data is fully local and open-format, but you read it through SiYuan (or its exports), not through any old editor.

If “my notes are just files” is a first principle for you, that decides it for Obsidian. If you’ve pushed Obsidian’s block links and Dataview far enough to feel the seams, SiYuan is what that workflow looks like when the whole app is designed for it. (And if you’re here shopping for an Obsidian alternative more broadly, our guide to second brain apps covers the whole field.)

SiYuan pricing vs Obsidian pricing — what you’ll actually pay

Both apps are free to use seriously, on your own device, with no note limits — the money is all in sync. The costs are less symmetric than they look:

• Obsidian: the app is free (a commercial license is optional at $50/user/year — encouraged, not required). Official Sync is $4/month billed annually ($5 monthly), end-to-end encrypted. The DIY crowd syncs free via iCloud, Syncthing or git, which works but is famously fiddly on mobile.
• SiYuan: a one-time $64 PRO purchase unlocks sync and backup to your own S3 or WebDAV storage — a few dollars a year at any cloud provider, encrypted before upload. The official cloud subscription with 8 GB runs $148/year, which is roughly three times Obsidian Sync.

So the cheapest serious multi-device setup is SiYuan plus your own bucket — pay once, own the pipeline. The simplest paid setup is Obsidian Sync. And SiYuan’s official cloud is the expensive option, not the budget one — worth knowing before you assume “open source” means cheaper everywhere. For the full SiYuan pricing breakdown — free tier, the PRO one-time license, the cloud subscription and self-hosting, line by line and dated — see the pricing table in our SiYuan vs Anytype comparison.

Plugins and community

Obsidian’s ecosystem is the largest in the category — roughly two thousand community plugins, an active forum and subreddit, and years of themes, tutorials and workflows for every niche. If you want something, someone has built it, documented it, and argued about it. The flip side: stock Obsidian is deliberately minimal, so the power features live in plugins you assemble and maintain yourself.

SiYuan inverts that. The core app ships what Obsidian users install plugins for — database and attribute views (Obsidian only recently added native Bases), spaced-repetition flashcards, PDF annotation, block embeds — and layers a smaller plugin marketplace on top. If your real comparison is SiYuan vs Notion, that’s the point: SiYuan is the closest thing to Notion’s blocks-and-databases model that runs entirely on your own disk (and if Notion is what you’re leaving, our Notion alternatives guide covers the field).

Development is very active (47,000+ GitHub stars; v3.8.9 shipped October 29, 2026, after v3.8.4 in September and the v3.8.0/v3.8.1 pair in August, with 3.8.10 alpha builds most days), but the community is smaller and Chinese-first: the app and docs are fully usable in English, while much of the forum activity isn’t. If built-in flashcards are a deciding factor, we’ve also compared SiYuan against Logseq, the other open-source contender there (the three-way SiYuan vs Logseq vs Obsidian question is answered on that page too) — and against Anytype, the other local-first, self-hostable one. The wider list of SiYuan alternatives is further down this page.

SiYuan vs Obsidian for self-hosting and developers

A large share of the people comparing these two are developers, and the SERP shows it: the top results ask which one to self-host and why engineers are switching. The honest split is this. Obsidian has no server component — there is nothing to self-host, because the vault is a folder you sync however you like (git, Syncthing, a NAS). SiYuan’s own docs call Docker “the easiest way to serve SiYuan on a server”: the whole app runs in a container and you use it from any browser, which is the closest thing in this category to a self-hosted Notion.

Querying is the other divide. Obsidian answers “show me every note tagged X modified this month” with the Dataview plugin or, since 2025, native Bases views over note properties. SiYuan ships an SQL query embed: because every paragraph is a block with an ID in a SQLite index, you write SQL against your own notes and embed the live result. That also explains the storage format question people search for — SiYuan documents are .sy files whose contents are JSON, not Markdown, so “grep my notes” is Obsidian’s win and “query my notes” is SiYuan’s. SiYuan’s block links are the block-level version of Obsidian’s file-level backlinks: a reference points at one paragraph, and follows it when the paragraph moves.

Neither offers a hosted web app. If you want your notes in a browser without running a server, SiYuan in Docker is the only route among the two — and a zero-install web workspace is a different category of tool (see the Dexi section below).

SiYuan vs Obsidian with an AI assistant (MCP)

Which of the two can an AI assistant actually use? As of November 2026 the answer favours SiYuan on paper. SiYuan ships a built-in MCP server inside its kernel — the same local service that runs the app, reached at its /mcp endpoint on port 6806 — authenticated with the workspace API token and, since v3.8.6 (September 2026), with OAuth 2.1 as well, so a remote client such as ChatGPT can sign in instead of pasting a token. The same release line added an in-app AI agent with its own tools (v3.8.9, October 29, 2026, pins agent sessions and reads embedded PDF images). Obsidian still has nothing official: the changelog through 1.15.1 (November 3, 2026) ships a CLI aimed at coding agents, not MCP. The community fills the gap — the Local REST API plugin serves an MCP endpoint at 127.0.0.1:27124/mcp behind an API key, and any filesystem MCP server can read the vault folder.

What neither gives you is a boundary. One SiYuan token or OAuth grant covers the whole workspace (a request for notebook-level MCP restrictions was closed unimplemented in November 2026), and an Obsidian API key reads every file in the vault except the configuration directory. 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.

Mobile experience

Obsidian’s iOS and Android apps are mature — the same vault, most plugins working, and a capture flow good enough to use as your daily notes app. Multi-device life is smoothest with paid Sync; iCloud works on Apple platforms, and Android DIY sync remains the community’s perennial thread.

SiYuan has real iOS and Android apps too (App Store, Play, and F-Droid), and they’re functional rather than polished: the desktop’s dense interface translates awkwardly to small screens, and multi-device use effectively requires setting up one of the paid sync paths first. If mobile is where most of your notes happen, that’s a genuine point for Obsidian; if your phone is mostly for capture and reading, SiYuan’s apps are entirely serviceable.

Getting your notes out

This audience reads exit clauses first, so: Obsidian has nothing to export. The vault already is the export — copy the folder and you’re done, which is the strongest portability story any notes app can offer.

SiYuan exports individual documents or whole notebooks to Markdown (plus PDF and other formats), and it’s good — but it is an export: block references flatten into text, and database views don’t survive the trip to plain files. Coming the other way, SiYuan imports Markdown folders, so an Obsidian vault’s text, headings and images come through cleanly. Expect to re-link, though: some [[wiki links]] resolve, plain Markdown links to other files often don’t, and plugin syntax — Dataview queries, Templater, Tasks metadata — arrives as literal text. The sane migration is a trial import of a copy of your vault, then an afternoon of link checking, not a one-click switch.

SiYuan alternatives: Logseq, Anytype, Capacities — and Obsidian

If you are weighing SiYuan alternatives, the best SiYuan alternatives each keep one thing SiYuan does and drop another. The short list, as of November 2026, each with its own comparison:

• Logseq — keeps the open-source license (AGPL-3.0) and the built-in flashcards, as an outliner on local files or its new local database (2.0.2, beta since October 2026). See SiYuan vs Logseq.
• Anytype — keeps local-first storage and adds end-to-end-encrypted sync for free, as typed objects rather than block documents; source-available, not open source. See SiYuan vs Anytype.
• Capacities — keeps the typed, Notion-like structure but moves it to the cloud: free sync, a paid Pro plan, no self-hosting. See Capacities vs SiYuan.
• Obsidian — the files answer: plain Markdown you own, the largest plugin ecosystem, no server — which is the rest of this page.