Filesystem (Reference) vs Desktop Commander

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

	Filesystem (Reference) Official MCP reference server for secure local filesystem read/write within allowed directories. Verified stdio (local) No auth TypeScript	Desktop Commander Powerful local filesystem + terminal MCP server: search, diff-edit files, and run shell commands. Verified stdio (local) No auth TypeScript
Category	Files & Storage	Files & Storage
Language	TypeScript	TypeScript
Transport	stdio (local)	stdio (local)
Auth	None	None
GitHub stars	74k	6.2k
Last commit	5 months ago	4 months ago
Verified
Actively maintained
Install	`npx -y @modelcontextprotocol/server-filesystem /absolute/path/to/dir`	`npx -y @wonderwhy-er/desktop-commander`
Repo	Open	Open

Verdict

Pick Filesystem (Reference) if you want the official, vendor-maintained server, and you prefer the more popular, battle-tested option.

Pick Desktop Commander if you prefer its approach (powerful local filesystem + terminal mcp server: search, diff-edit files, and run shell commands).

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"
      ]
    }
  }
}

Add Desktop Commander

Install / run

npx -y @wonderwhy-er/desktop-commander

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

{
  "mcpServers": {
    "desktop-commander": {
      "command": "npx",
      "args": [
        "-y",
        "@wonderwhy-er/desktop-commander"
      ]
    }
  }
}

FAQ

Filesystem (Reference) or Desktop Commander — which is better?

Pick Filesystem (Reference) if you want the official, vendor-maintained server, and you prefer the more popular, battle-tested option. Pick Desktop Commander if you prefer its approach (powerful local filesystem + terminal mcp server: search, diff-edit files, and run shell commands).

Can I use both Filesystem (Reference) and Desktop Commander?

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 Filesystem (Reference) and Desktop Commander work with Claude, Cursor and Windsurf?

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

View Filesystem (Reference) →View Desktop Commander →More comparisons →