How to Use MCP with Claude Desktop

OVERVIEW Claude Desktop was among the first mainstream clients to ship native Model Context Protocol (MCP) support. MCP lets Claude launch companion processes — official reference servers for files, memory, Git, web fetch, time, reasoning, and more — and call their tools during conversations. This guide follows configuration patterns from the official modelcontextprotocol/servers README at https://github.com/modelcontextprotocol/servers. Install commands below are copied from that repository, not invented. WHAT MCP DOES IN CLAUDE DESKTOP When Claude Desktop starts, it reads claude_desktop_config.json, spawns each configured MCP server as a subprocess, and communicates over stdio using the MCP protocol. Tools appear in the UI; Claude decides when to invoke them based on your prompts. Resources and prompts are also supported by some servers (the Everything reference server demonstrates all three). PREREQUISITES Install runtimes before configuring servers: - Node.js 18+ for npx servers: @modelcontextprotocol/server-filesystem, server-memory, server-sequential-thinking, server-everything - uv / uvx for Python servers: mcp-server-git, mcp-server-fetch, mcp-server-time Official standalone examples from the README: npx -y @modelcontextprotocol/server-memory npx -y @modelcontextprotocol/server-filesystem /path/to/allowed/dir uvx mcp-server-git --repository path/to/git/repo uvx mcp-server-fetch uvx mcp-server-time npx -y @modelcontextprotocol/server-sequential-thinking npx -y @modelcontextprotocol/server-everything CONFIG FILE LOCATION - macOS: ~/Library/Application Support/Claude/claude_desktop_config.json - Windows: %APPDATA%\Claude\claude_desktop_config.json - Linux: ~/.config/Claude/claude_desktop_config.json Create the file if missing with { "mcpServers": {} }. OFFICIAL CONFIG FORMAT From the README: { "mcpServers": { "memory": { "command": "npx", "args": ["-y", "@modelcontextprotocol/server-memory"] } } } MULTI-SERVER EXAMPLE (FROM README) { "mcpServers": { "filesystem": { "command": "npx", "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/allowed/files"] }, "git": { "command": "uvx", "args": ["mcp-server-git", "--repository", "path/to/git/repo"] } } } WINDOWS NOTE (OFFICIAL) On Windows, wrap npx with cmd /c: { "mcpServers": { "memory": { "command": "cmd", "args": ["/c", "npx", "-y", "@modelcontextprotocol/server-memory"] } } } Apply the same pattern to every npx-based server. Leave uvx entries unchanged. STEP-BY-STEP SETUP 1. Install Node and uv. 2. Test one server in Terminal/PowerShell with the standalone command. 3. Edit claude_desktop_config.json with valid JSON. 4. Quit Claude Desktop fully (system tray on Windows). 5. Relaunch and start a new chat. 6. Confirm MCP tools indicator shows connected servers. 7. Ask Claude to use a tool explicitly ("List files in my allowed directory using MCP"). SECURITY NOTES The README warns reference servers are educational, not production-ready. Scope Filesystem directories narrowly. Use env blocks in config for secrets on servers that need tokens (README shows GITHUB_PERSONAL_ACCESS_TOKEN pattern for archived GitHub server — prefer maintained community servers for GitHub today). Never commit claude_desktop_config.json with secrets to git. FAQ Q: Server not connecting? A: Run the command manually; fix PATH issues; validate JSON. Q: Where are commands documented? A: https://github.com/modelcontextprotocol/servers Q: Can I use Docker? A: Filesystem README documents Docker — advanced; NPX is the README Getting Started default. CURSOR / CLINE NOTE This tutorial targets Claude Desktop specifically. Cursor uses mcp.json; Cline uses extension MCP settings — patterns are similar but paths differ. See client guides on this directory for those IDEs. TROUBLESHOOTING Check Claude logs if available on your platform. Common failures: missing Node, unescaped Windows paths, forgetting to restart Claude, firewall blocking uvx downloads on first run. UNDERSTANDING MCP SERVER TYPES IN THE OFFICIAL REPO TypeScript servers (npx): Everything, Filesystem, Memory, Sequential Thinking. Python servers (uvx): Fetch, Git, Time. This split matters for prerequisites — install both Node and uv for the full reference set. The README Getting Started section demonstrates Memory as the simplest first server because it needs no path arguments. ENVIRONMENT VARIABLES IN CONFIG The README multi-server example shows env blocks for servers requiring tokens (GitHub PAT example). Active reference servers mostly need no secrets except path arguments. Community servers often require API keys — use env in mcpServers entries rather than embedding secrets in prompts. RECOMMENDED FIRST PROJECT STACK For software work in Claude Desktop, start with Filesystem scoped to one repo, add Git with matching --repository, add Memory for decisions, add Fetch for external docs. Add Sequential Thinking when planning complex refactors. Add Time when scheduling across zones. Add Everything only when debugging MCP itself. RESTART DISCIPLINE Claude Desktop caches running MCP processes. Editing config without quitting the app often leaves stale servers connected. On Windows, check the system tray for Claude background processes. On macOS, Cmd+Q fully exits. PROTOCOL RESOURCES Learn client concepts like Roots at https://modelcontextprotocol.io — especially relevant for Filesystem dynamic directories. The specification explains tools, resources, prompts, and notifications that Everything demonstrates. COMPARING CLAUDE TO OTHER CLIENTS Claude Desktop uses claude_desktop_config.json with mcpServers key. Cursor uses mcp.json. Cline embeds config in the extension. Command and args arrays remain portable — only file location and restart procedures differ. This portability is intentional in the MCP design: servers are client-agnostic stdio processes. LONG-TERM MAINTENANCE Pin versions in args only if you fork servers — official README uses -y for latest npm and uvx resolution. Monitor modelcontextprotocol/servers releases for breaking changes. Reference servers carry MIT/Apache licenses but no enterprise SLA — plan upgrades in dev environments first.