MarkItDown MCP vs Filesystem (Reference)

A side-by-side comparison of two Files & Storage servers — tools, transport, auth, maintenance, and copy-paste config for each.

	MarkItDown MCP Give your agent Microsoft's MarkItDown: convert PDFs, Office docs, images, and URLs into LLM-ready Markdown. Unverified stdio (local) No auth Python	Filesystem (Reference) Official MCP reference server for secure local filesystem read/write within allowed directories. Verified stdio (local) No auth TypeScript
Category	Files & Storage	Files & Storage
Language	Python	TypeScript
Transport	stdio (local)	stdio (local)
Auth	None	None
GitHub stars	162k	74k
Last commit	8 days ago	5 months ago
Verified
Actively maintained
Install	`pip install markitdown-mcp`	`npx -y @modelcontextprotocol/server-filesystem /absolute/path/to/dir`
Repo	Open	Open

Verdict

Pick MarkItDown MCP if you prefer the more popular, battle-tested option.

Pick Filesystem (Reference) if you need the broadest set of tools, and you want a verified, documented setup.

Add MarkItDown MCP

Install / run

pip install markitdown-mcp

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "markitdown-mcp": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "markitdown-mcp:latest"
      ]
    }
  }
}

Requires Docker to be installed and running.

Add Filesystem (Reference)

Install / run

npx -y @modelcontextprotocol/server-filesystem /absolute/path/to/dir

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "filesystem-reference": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/absolute/path/to/dir"
      ]
    }
  }
}

FAQ

MarkItDown MCP or Filesystem (Reference) — which is better?

Pick MarkItDown MCP if you prefer the more popular, battle-tested option. Pick Filesystem (Reference) if you need the broadest set of tools, and you want a verified, documented setup.

Can I use both MarkItDown MCP and Filesystem (Reference)?

Yes — MCP clients let you enable multiple servers at once. Add both configs to your client's mcpServers and use whichever tool fits the task.

Do MarkItDown MCP and Filesystem (Reference) work with Claude, Cursor and Windsurf?

Both do. Copy the per-client config below into Claude Desktop, Cursor, or Windsurf.

View MarkItDown MCP →View Filesystem (Reference) →More comparisons →