SiYuan

What SiYuan does

SiYuan is a personal knowledge base in which every paragraph, heading or list item is a block with its own identity. Blocks can be referenced, embedded in other documents and linked both ways, and they can carry custom attributes. Documents are written in a WYSIWYG editor that uses Markdown syntax, with outlines, zooming into a single block, and support for very long documents.

On top of that core the app bundles a lot: math, charts, flowcharts and Gantt diagrams; a database table view; flashcards with spaced repetition; PDF annotation with links back to the source; OCR through Tesseract; and AI writing and question answering through an OpenAI-compatible API. For power users, SQL queries can be embedded in a document to list blocks that match conditions, which turns notes into a queryable database.

Data and formats

SiYuan is local-first: notes stay on your device unless you set up sync. It stores documents in its own JSON-based format and keeps a SQLite index for search, rather than writing plain Markdown files. Markdown (with assets), PDF, Word and HTML are export formats. This is a real difference from Markdown-folder apps: you can get your notes out, but other editors cannot work on the same files day to day.

Self-hosting SiYuan

The desktop apps need no server. SiYuan can also run in Docker for access from a browser; the container needs a mounted workspace folder and an access code or OIDC login, and a reverse proxy must pass WebSocket traffic on /ws. The README lists the limits of this mode: browser use only, the desktop and mobile apps cannot connect to it, and PDF, HTML and Word export and Markdown import are not available. A community Helm chart exists for Kubernetes.

Sync and the paid membership

Sync is where the business model sits. Syncing between devices through the official cloud is part of a paid annual subscription, and syncing or backing up to your own S3 or WebDAV storage requires a paid one-time PRO purchase. The README also says that syncing the data folder through third-party sync folders is not supported. Local use on one device costs nothing.

Limitations

Multi-device use effectively requires paying, even if you bring your own storage. The proprietary storage format makes it harder to move notes to another tool than with Markdown-based apps. The Docker mode is a browser-only interface with missing features, not a sync server. SiYuan is a single-user tool and not a team wiki.

Who it suits

SiYuan suits people who want fine-grained block references, queries and study tools such as flashcards in one local app, and who are happy to pay for sync. If plain Markdown files are a priority, look at Logseq; if free self-hosted sync matters more, Trilium Notes is the closer fit.