Guide · Updated May 2026

How to use Claude Desktop with your Markdown notes.

Claude Desktop became powerful in 2025 when MCP — the Model Context Protocol — landed. Suddenly your $20/month Claude subscription could read files, run tools, and act on your local system. The most useful version of that, by a wide margin, is "let Claude read my notes." Here's how, in two flavors: the no-config Eyrie path, and the manual filesystem-server path.

What is MCP, briefly?

Model Context Protocol is an open spec (released by Anthropic in late 2024) that lets AI clients like Claude Desktop talk to external "servers" that provide tools and data. Think of it as a USB port for AI clients — the client doesn't need to know in advance what's plugged in, it just discovers the available tools and uses them.

For Markdown notes, the relevant MCP servers are:

• Filesystem server (official, generic) — gives Claude read/write access to a folder.
• Eyrie's MCP server (built for vaults) — adds semantic search, backlinks, tag retrieval, and a diff-before-write approval flow.

Path A: Eyrie's one-click setup.

1. Download Eyrie and open it.
2. Open the folder containing your Markdown notes (Obsidian vault, exported Notion folder, or any directory of .md files).
3. Settings → MCP → click "Install in Claude Desktop."
4. Eyrie writes the right config into ~/Library/Application Support/Claude/claude_desktop_config.json.
5. Restart Claude Desktop. You'll see Eyrie's tools in the MCP tools list.

What Claude can now do:

• Search your vault by keyword, semantic similarity, or both. ("Find everything I've written about onboarding flows.")
• Get backlinks for any note. ("What notes mention vantar-energy.md?")
• List tags across the vault. ("What are my top 20 tags?")
• Fetch URLs via Jina Reader, strip noise, save as a Markdown note.
• Propose edits — Claude writes a diff that Eyrie shows you for approval before anything touches disk.

Path B: Manual filesystem server.

If you don't want Eyrie or you're not on a Mac, you can use Anthropic's reference filesystem server.

1. Make sure Node.js is installed (node --version should print 18+).
2. Open ~/Library/Application Support/Claude/claude_desktop_config.json in a text editor.
3. Add this configuration (replace /Users/you/Notes with your actual notes path):

{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/Users/you/Notes"
      ]
    }
  }
}

4. Restart Claude Desktop.
5. You should see filesystem tools available — Claude can list, read, write, search files in that folder.

What you lose compared to Eyrie: no semantic search (just file listing and grep), no backlink awareness, no diff-before-write approval (Claude writes directly), no tag aggregation, no URL fetching.

What works well, what doesn't.

Works well:

• "Summarize my notes from this week" → Claude opens your daily notes, reads them, drafts a summary.
• "Find every note where I mentioned X person" → keyword + semantic search, returns sourced answers.
• "Draft a blog post combining these three notes" → Claude pulls content from each file, structures a draft.
• "What are the open questions in my project notes?" → Claude reads project files, extracts unresolved threads.

Doesn't work as well:

• "Reorganize my whole vault" — Claude is good at incremental edits, terrible at large-scale reorganizations. It loses track of cross-references.
• Anything that needs the vault's full graph in context — Claude can only see what it pulls into the conversation. 5,000-note vaults don't fit.
• Real-time multi-user collaboration — MCP is a single-client protocol.

Privacy notes.

When Claude Desktop reads a note via MCP, the contents of that note are sent to Anthropic's API as part of the conversation. The whole note. If you have notes you don't want Anthropic to ever see, scope your MCP server to a subdirectory that excludes them, or use Eyrie's file-allowlist in Settings → MCP → Advanced.

None of this is unique to MCP — any AI integration with your notes has the same trust model. But it's worth understanding before pointing Claude at your most private folder.

FAQ