# Open source Obsidian alternatives for AI agents

3 alternatives to Obsidian. 3 have an interface an agent can drive. 3 are open source.

Page: alternatives/obsidian.html

## SiYuan

Block-based local-first knowledge base whose Go kernel ships a 30-plus tool MCP server and HTTP API.

- Listing: apps/siyuan-note--siyuan.html
- JSON: apps/siyuan-note--siyuan.json
- License: AGPL-3.0
- Agent interface: MCP server, from the builder
- Reach: 9 of 10 jobs
- Last activity: 2026-09-03
- Effort: config-only
- Agent cannot reach: Plugins and marketplace, AI writing UI
- Use it when: you want block references and databases like Notion, stored locally, with an agent that can query them by SQL
- Use it when: you run a Docker kernel on your NAS and want daily notes written by an agent from the terminal
- Gotcha: AGPL-3.0
- Gotcha: Since v3.7.0 the Docker image needs an explicit serve subcommand
- Gotcha: Official cloud sync and some features are paid; third-party S3/WebDAV sync needs PRO Features
- Gotcha: Docker web UI is protected only by the access auth code unless OIDC is set

## Trilium Notes

Hierarchical note tree with attributes and scripting, driven by the ETAPI REST API and an in-repo MCP route.

- Listing: apps/triliumnext--trilium.html
- JSON: apps/triliumnext--trilium.json
- License: AGPL-3.0
- Agent interface: API and MCP server, from the builder
- Reach: 8 of 10 jobs
- Last activity: 2026-09-03
- Effort: config-only
- Agent cannot reach: Scripting and widgets; Sync and protected (encrypted) notes
- Use it when: you want a deeply nested personal or team knowledge tree that an agent can populate through a stable REST API
- Use it when: you outgrew flat markdown folders and want attributes, relations, and saved searches
- Gotcha: AGPL-3.0
- Gotcha: The desktop app and server versions must match for sync; disable auto-updates on the server when using TriliumDroid
- Gotcha: ETAPI needs a token created in the UI (Options > ETAPI) or from POST /etapi/auth/login with the instance password
- Gotcha: MCP route tool names were not read; they come from the core LLM tool registry (packages/core llm/tools)

## Tolaria

Files-first markdown second brain with git built in and an in-repo MCP server for Claude Code and Codex.

- Listing: apps/refactoringhq--tolaria.html
- JSON: apps/refactoringhq--tolaria.json
- License: AGPL-3.0
- Agent interface: MCP server, from the builder
- Reach: 4 of 8 jobs
- Last activity: 2026-09-03
- Agent cannot reach: Git commit, push, and history; In-app AI chat over note context; Inbox and web-resource capture
- Use it when: you want your notes as plain markdown in git and an agent that can search and write them from Claude Code
- Use it when: you run a 10,000-note personal vault and want keyboard-first navigation with AI on the side
- Gotcha: AGPL-3.0-or-later
- Gotcha: The MCP server talks to the running desktop app over a websocket bridge; open_note and vault attach need the app open
- Gotcha: No paid or hosted edition; sync is whatever git remote you choose

## Questions

### Is there an open source alternative to Obsidian?

Yes. All 3 listings here are open source: SiYuan (AGPL-3.0), Trilium Notes (AGPL-3.0), Tolaria (AGPL-3.0).

### Which Obsidian alternatives have an MCP server?

SiYuan, Trilium Notes and Tolaria have MCP servers from their builders.

### Which Obsidian alternative can an agent do the most with?

SiYuan: 9 of 10 recorded jobs reachable. Jobs differ by listing, so read each list before you choose.