Best Self Hosted Alternatives to SiYuan

Joplin is a free and open source note-taking and to-do application designed for keeping your data private while staying available across devices. It is offline-first and can sync using end-to-end encryption via multiple backends, including WebDAV and Nextcloud.

Key Features

• Organize notes in notebooks with tags and powerful full-text search
• Markdown-based notes with optional rich-text editing
• End-to-end encryption (E2EE) for sync to protect note contents
• Sync with multiple providers and standards (including WebDAV-compatible services)
• Web Clipper extension to save web pages or screenshots as notes
• Import from Evernote (ENEX) and import/export Markdown
• Customization via plugins, themes, and an extension API
• Available on desktop and mobile, plus a terminal application

Use Cases

• Personal knowledge management across devices with encrypted synchronization
• Migrating from Evernote and consolidating notes into an open format
• Capturing research and articles via web clipping for offline reading

Joplin fits individuals and teams that want flexible note organization, broad sync options, and strong privacy controls. Its open formats and extensibility make it a solid long-term notes and knowledge base solution.

SiYuan is a privacy-focused, open-source personal knowledge management application that organizes content as editable blocks and supports Markdown WYSIWYG. It emphasizes local-first storage with optional end-to-end encrypted synchronization and offers desktop, mobile and Docker deployments. (b3log.org)

Key Features

• Block-based editor with block-level references and two-way links for fine-grained connections.
• Markdown WYSIWYG editing plus large-document (million-word) editing with dynamic loading.
• Built-in database/table view, SQL query embeds and template/snippet support.
• Spaced-repetition flashcards and AI-assisted writing/Q&A via external model APIs.
• OCR support (Tesseract), PDF annotation linking and rich embeds (charts, flowcharts, math).
• Multiple sync options including end-to-end encrypted sync, S3 and WebDAV backends, and Docker deployment. (readmex.com)

Use Cases

• Personal knowledge management and research notes with block-level linking for networked thought.
• Publishing and documentation workflows where notes are exported to standard Markdown, HTML or platform-targeted formats.
• Shared team knowledge bases or a self-hosted notes server accessible via Docker and mobile/desktop clients.

Limitations and Considerations

• Some member-only features require payment; the project notes that some capabilities are gated for paid members. (github.com)
• Community discussions and repository issues have raised concerns about telemetry defaults and the need for careful plugin vetting; administrators should review telemetry and plugin settings for privacy-sensitive deployments. (github.com)

SiYuan combines a block-first editor model with server-backed features (Docker, APIs, sync) and desktop/mobile clients, making it suitable for users who want a privacy-oriented, extensible PKM system. Its active open-source repository and plugin ecosystem support customization, but administrators should review paid-feature gating and telemetry settings before production use. (b3log.org)

Logseq is a privacy-first platform for personal knowledge management built around linked, block-based notes organized as a graph. It supports local-first workflows using Markdown or Org-mode files, with additional options for database-backed graphs and real-time collaboration.

Key Features

• Block-based outlining with bidirectional linking and graph-based navigation
• Local file-based graphs using Markdown and Org-mode for longevity and portability
• Task management features integrated into notes (e.g., TODO workflows and queries)
• Whiteboards for spatial thinking with shapes, connectors, drawings, and embeds
• PDF reading and annotation integrated into the knowledge base
• Plugin and theme ecosystem via a dedicated plugin API
• Optional database-backed graphs with sync and real-time collaboration capabilities

Use Cases

• Personal knowledge base for research notes, study, and writing workflows
• Daily journaling and task tracking with linked context across projects
• Team knowledge sharing and collaborative note-taking (where collaboration is enabled)

Limitations and Considerations

• Database-backed graphs and real-time collaboration features may be in beta/alpha and can carry higher risk of data issues; backups are recommended

Logseq is well-suited for users who want a durable, local-first note system with strong linking and outlining. Its whiteboards, PDF annotation, and extensibility make it flexible for both personal productivity and collaborative knowledge work.

TagSpaces is an offline-first, cross-platform application for organizing and managing local files using a flexible tagging system. It works without accounts or a central cloud backend by storing metadata alongside your files, keeping your data portable and private.

Key Features

• Tag files and folders using filename tags or sidecar metadata files
• Fast filtering and search, including a local index service for content search
• Built-in viewers and editors for common formats (text, Markdown, HTML, media)
• Note-taking and simple task lists stored as plain files
• Web Clipper browser extension to save web pages, screenshots, and bookmarks as local files
• Extensible architecture via custom viewers/editors (plugins)
• Optional local AI/LLM integrations (via Ollama) for summarization, tagging, and annotation

Use Cases

• Organize a personal document archive (PDFs, receipts, manuals) with consistent tags
• Build an offline personal knowledge base with notes, web clippings, and media
• Create a portable file-based workspace that can be synced with third-party tools

Limitations and Considerations

• Not optimized for working locations containing more than about 100,000 files

TagSpaces is well-suited for users who want a file-based, vendor-neutral way to manage documents, notes, and media. Its offline design and optional local AI features make it a strong choice for privacy-focused personal and small-team workflows.

Nextcloud Notes is a simple, distraction-free note-taking application for Nextcloud. It stores notes as regular files in your Nextcloud, making them accessible and syncable across Nextcloud clients and devices.

Key Features

• Notes stored as files in your Nextcloud (compatible with Nextcloud sync clients)
• Markdown formatting support for writing and previewing
• Categories for organizing notes
• Favorites for quick access to important notes
• JSON-based REST API for integrations and mobile/third-party clients
• Admin defaults configurable via Nextcloud occ commands (mode, file extension, default folder)

Use Cases

• Personal note-taking synced across desktop and mobile via Nextcloud
• Team or shared note folders managed through Nextcloud file sharing
• Integrating notes into custom apps via the Notes REST API

Nextcloud Notes is a good fit if you want lightweight notes that remain plain files inside your Nextcloud storage, while still providing a focused editor, Markdown support, and an integration-friendly API.

Silicon Notes is a lightweight, low-friction personal knowledge base and wiki-style note app. It provides plaintext Markdown editing with HTML rendering, a simple no-frills UI, and tools for organizing and searching pages.

Key Features

• Markdown-based editing with rendered HTML and syntax highlighting for code blocks
• Bi-directional page relationships (backlinks) and an in-page table of contents sidebar
• Full-text and title search for fast retrieval of notes
• Page history and revision tracking for auditing and rollback
• Export and import of pages and revisions as JSON for portability
• Optional CodeMirror editor for enhanced editing experience; configurable editor via environment
• Simple deployment options: SQLite-backed instance, container images and docker-compose samples

Use Cases

• Personal knowledge base for developers, researchers, or hobbyists who prefer Markdown
• Lightweight wiki for a small team on a private LAN or VPN-protected server
• Archival and searchable notes with revision history and portable JSON exports

Limitations and Considerations

• No built-in authentication or authorization; intended for trusted/private networks or behind reverse proxies with access control
• Default SQLite storage may limit scalability for larger teams or high-concurrency environments
• Optional CodeMirror assets add frontend weight and must be installed separately if enabled

Silicon Notes is suited for users seeking a simple, self-contained note/wiki app focused on Markdown, searchability, and minimal operational complexity. It emphasizes portability and ease of deployment over enterprise features and multi-tenant access control.