Debugging - Model Context Protocol(MCP)

A comprehensive guide to debugging Model Context Protocol (MCP) integrations

Effective debugging is essential when developing MCP servers or integrating them with applications. This guide covers the debugging tools and approaches available in the MCP ecosystem.

This guide is for macOS. Guides for other platforms are coming soon.

Debugging tools overview

MCP provides several tools for debugging at different levels:

MCP Inspector

Interactive debugging interface

Direct server testing

See the Inspector guide for details

Claude Desktop Developer Tools

Integration testing

Log collection

Chrome DevTools integration

Server Logging

Custom logging implementations

Error tracking

Performance monitoring

Debugging in Claude Desktop

Checking server status

The Claude.app interface provides basic server status information:

Click the

icon to view:

Connected servers

Available prompts and resources

Click the

icon to view:

Tools made available to the model

Viewing logs

Review detailed MCP logs from Claude Desktop:

Copy

The logs capture:

Server connection events

Configuration issues

Runtime errors

Message exchanges

Using Chrome DevTools

Access Chrome’s developer tools inside Claude Desktop to investigate client-side errors:

Create a developer_settings.json file with allowDevTools set to true:

Open DevTools: Command-Option-Shift-i

Note: You’ll see two DevTools windows:

Main content window

App title bar window

Use the Console panel to inspect client-side errors.

Use the Network panel to inspect:

Message payloads

Connection timing

Common issues

Working directory

When using MCP servers with Claude Desktop:

The working directory for servers launched via claude_desktop_config.json may be undefined (like / on macOS) since Claude Desktop could be started from anywhere

Always use absolute paths in your configuration and .env files to ensure reliable operation

For testing servers directly via command line, the working directory will be where you run the command

For example in claude_desktop_config.json, use:

{
  "command": "npx",
  "args": ["-y", "@modelcontextprotocol/server-filesystem", "/Users/username/data"]
}

Instead of relative paths like ./data

Environment variables

MCP servers inherit only a subset of environment variables automatically, like USER, HOME, and PATH.

To override the default variables or provide your own, you can specify an env key in claude_desktop_config.json:

{
  "myserver": {
    "command": "mcp-server-myapp",
    "env": {
      "MYAPP_API_KEY": "some_key",
    }
  }
}

Server initialization

Common initialization problems:

Path Issues

Incorrect server executable path

Missing required files

Permission problems

Try using an absolute path for command

Configuration Errors

Invalid JSON syntax

Missing required fields

Type mismatches

Environment Problems

Missing environment variables

Incorrect variable values

Permission restrictions

Connection problems

When servers fail to connect:

Check Claude Desktop logs

Verify server process is running

Test standalone with Inspector

Verify protocol compatibility

Implementing logging

Server-side logging

When building a server that uses the local stdio transport, all messages logged to stderr (standard error) will be captured by the host application (e.g., Claude Desktop) automatically.

Local MCP servers should not log messages to stdout (standard out), as this will interfere with protocol operation.

For all transports, you can also provide logging to the client by sending a log message notification:

Python

TypeScript

Important events to log:

Initialization steps

Resource access

Tool execution

Error conditions

Performance metrics

Client-side logging

In client applications:

Enable debug logging

Monitor network traffic

Track message exchanges

Record error states

Debugging workflow

Development cycle

Initial Development

Use Inspector for basic testing

Implement core functionality

Add logging points

Integration Testing

Test in Claude Desktop

Monitor logs

Check error handling

Testing changes

To test changes efficiently:

Configuration changes: Restart Claude Desktop

Server code changes: Use Command-R to reload

Quick iteration: Use Inspector during development

Best practices

Logging strategy

Structured Logging

Use consistent formats

Include context

Add timestamps

Track request IDs

Error Handling

Log stack traces

Include error context

Track error patterns

Monitor recovery

Performance Tracking

Log operation timing

Monitor resource usage

Track message sizes

Measure latency

Security considerations

When debugging:

Sensitive Data

Sanitize logs

Protect credentials

Mask personal information

Access Control

Verify permissions

Check authentication

Monitor access patterns

Getting help

When encountering issues:

First Steps

Check server logs

Test with Inspector

Review configuration

Verify environment

Support Channels

GitHub issues

GitHub discussions

Providing Information

Log excerpts

Configuration files

Steps to reproduce

Environment details