Problem

Currently, all MCP servers defined in claude_desktop_config.json are automatically enabled when Claude Desktop starts. There's no native way to temporarily disable a server without completely removing its configuration from the file or manually toggling the MCP in the chat interface.

This creates friction when:

• Testing new MCP servers that may be unstable
• Managing multiple servers where some should remain configured but not always active
• Wanting to reduce context token usage from unused MCP tools
• Debugging issues by selectively enabling/disabling servers
• Maintaining different configurations for different workflows

Proposed Solution

Add an optional enabled boolean parameter to the MCP server configuration that defaults to true:

{
  "mcpServers": {
    "Arc SLURM MCP": {
      "enabled": true,
      "command": "uv",
      "args": ["run", "/path/to/server"],
      "env": {},
      "transport": "stdio"
    },
    "Arc Cloud Run MCP": {
      "enabled": false,  // Disabled by default
      "command": "uv",
      "args": ["run", "/path/to/other/server"],
      "env": {
        "GCP_PROJECT_ID": "my-project"
      },
      "transport": "stdio"
    }
  }
}

Benefits

1. Better developer experience: Keep all server configurations in one place without needing to comment/uncomment or maintain separate config files
2. Easier testing: Quickly toggle servers on/off during development
3. Context management: Control token usage by disabling unused servers
4. Configuration as documentation: Keep disabled servers as examples/documentation
5. Workflow flexibility: Different configurations for different use cases without file swapping

Current Workarounds

Users currently must:

• Completely remove and re-add server configurations
• Maintain multiple config files and swap them
• Use external tools like yq with YAML conversion (as documented in [zudochkin/disable-claude-mcp](https://github.com/zudochkin/disable-claude-mcp))

Related

• Similar feature request for Claude Code: [Feature Request] MCP Server Enable/Disable Toggle anthropics/claude-code#4879
• This request specifically targets Claude Desktop's configuration format

Additional Context

This feature would align with standard configuration practices in other tools where services/plugins can be defined but selectively enabled.