How I Resolved a Critical Claude Desktop MCP Server Configuration Issue with a Simple Solution

Have you ever encountered a technical issue that seemed completely baffling, only to discover the solution was surprisingly simple? Recently, I faced this exact situation while setting up the MCP filesystem server for Claude Desktop on my Mac.

The Challenge: Mysterious Configuration Failures

While the mcp-server-sqlite with uvx worked flawlessly, I hit a roadblock when trying to configure the filesystem server using claude_desktop_config.json. My attempts to use both npx and node directly resulted in unexpected errors that left me puzzled.

First Attempt: The NPX Approach

My first configuration looked straightforward enough:

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

However, the logs revealed a peculiar error:

==> /Users/xxx/Library/Logs/Claude/mcp-server-filesystem.log <==
command not found: /Users/xxx/Desktop

Strangely, running the identical command directly in the terminal worked perfectly:

npx @modelcontextprotocol/server-filesystem '/Users/xxx/Desktop'
# Output: Secure MCP Filesystem Server running on stdio... Allowed directories: [...]

Second Attempt: The Node Direct Approach

For my next approach, I tried using Node.js directly:

{
  "mcpServers": {
    "filesystem": {
      "command": "node",
      "args": [
        "/usr/local/lib/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js",
        "/Users/xxx/Desktop"
      ]
    }
  }
}

Yet this produced a syntax error:

==> /Users/xxx/Library/Logs/Claude/mcp-server-filesystem.log <==
/usr/local/lib/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js:2
import { Server } from "@modelcontextprotocol/sdk/server/index.js";
       ^

SyntaxError: Unexpected token {
    at Module._compile (internal/modules/cjs/loader.js:723:23)
    ...

Again, running the exact same command in the terminal worked without issues.

At this point, I was stumped. Was it a path issue? I even tried specifying the full path to node (for example, /usr/local/bin/node) in the configuration file, which seemed to work temporarily—but it was only a fragile workaround, not a real solution.

The Unexpected Solution: Version Conflicts

After considerable troubleshooting, I discovered the root cause: outdated Node.js versions lurking in my system.

While my default terminal Node was up-to-date, older versions (likely managed by nvm) were somehow interfering when Claude attempted to launch the server through the configuration file.

The Simple Fix That Saved the Day

The solution was remarkably straightforward: I removed the old Node.js installations, ensuring only a modern version remained on my system.

The result? Both the npx and node configurations in claude_desktop_config.json began working perfectly, with no errors or confusion—just seamless filesystem access through MCP.

What You Can Learn From This Experience

If you encounter situations where commands work flawlessly in your terminal but fail when launched from another application, consider checking for version conflicts in your runtime environments.

Sometimes the most powerful fix is the simplest one: cleaning up outdated versions of your development tools.

Have you experienced similar phantom issues with conflicting software versions? I'd love to hear about your troubleshooting wins in the comments below.