Turn Obsidian into a JARVIS with Claude Code and MCP

Your Obsidian vault is already a folder of Markdown files. Wire it up to Claude Code with MCP and Claude can search your notes, pull context from past research, create new entries, and link ideas together, all from the terminal.

Option 1: Run Claude Code from Your Vault

The simplest approach. cd into your vault and run Claude Code directly:

cd ~/Documents/MyVault
claude

Drop a CLAUDE.md at the vault root with instructions about your note structure, tagging conventions, and preferred templates. Claude reads this on every startup, so it knows your system before you type anything.

Option 2: MCP Server (Access Vault from Any Directory)

Install the Obsidian MCP plugin so Claude can reach your vault from any project:

{
  "mcpServers": {
    "obsidian": {
      "command": "npx",
      "args": ["-y", "obsidian-claude-code-mcp"]
    }
  }
}

Add this to ~/.claude/settings.json under mcpServers. The plugin auto-discovers local vaults via WebSocket on port 22360. You’ll need the companion Obsidian plugin installed and running.

Option 3: Filesystem MCP (No Plugin Required)

Skip the Obsidian plugin entirely and point the filesystem MCP server at your vault:

{
  "mcpServers": {
    "obsidian-vault": {
      "command": "npx",
      "args": ["-y", "@anthropic/mcp-filesystem", "/Users/you/Documents/MyVault"]
    }
  }
}

Claude gets read/write access to every note. No Obsidian plugin needed since it’s just files.

The JARVIS Setup

The real power comes from combining your vault with Claude’s memory system. Structure your vault so Claude can use it as persistent memory:

MyVault/
├── CLAUDE.md           # Instructions for Claude
├── 00-inbox/           # Quick captures Claude can triage
├── 01-projects/        # Active project notes
├── 02-areas/           # Ongoing responsibilities
├── 03-resources/       # Reference material
├── 04-archive/         # Completed work
└── journal/            # Daily notes Claude can reference

In your CLAUDE.md, tell Claude how to use the vault:

## Vault Rules
- Search 03-resources/ before answering research questions
- When I finish a project, move its notes to 04-archive/
- Create new notes in 00-inbox/ with [[wikilinks]] to related notes
- Read journal/ entries for context on what I've been working on
- Tag all new notes with the date and relevant topic tags

Now Claude pulls from your past research before answering, files new knowledge into the right folder, and maintains links between concepts. You ask a question, and it checks what you already know first.

Tip

Add a daily note template that Claude populates with a summary of what you worked on together. Run it as a hook on session end and your vault becomes an automatic work log.