Debugging

Source: MCP 89153404

python3 inspector_smoke.py --call add --arg a=2 --arg b=3 --check-stdout -- python3 sdk_server.py stdio ok
python3 inspector_smoke.py --check-stdout -- python3 sdk_server.py stdio banner
python3 inspector_smoke.py --check-stdout -- python3 sdk_server.py stdio crash

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.

Debugging tools overview

MCP provides several tools for debugging at different levels:

1. MCP Inspector: interactive, transport-agnostic testing UI. Connect to stdio or Streamable HTTP servers, invoke tools, prompts, and resources, and watch the notification stream. This should be your first stop.
2. Server logging: structured logs to stderr (stdio transport) or via OpenTelemetry (all transports). Logging over the protocol (notifications/message) is deprecated as of protocol version 2026-07-28.
3. Client developer tools: most MCP clients expose logs and connection state. See Debugging in Claude Desktop below for one example, or consult your client’s documentation.

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 automatically.

For servers using the Streamable HTTP transport, stderr is not captured by the client. Use your own server-side log aggregation or OpenTelemetry for logs, and standard HTTP tooling (curl, browser DevTools Network panel) to inspect requests and SSE streams.

For all transports, record what the server is doing as it runs:

import logging

from mcp.server import MCPServer

logger = logging.getLogger(__name__)

mcp = MCPServer("reports")


@mcp.tool()
async def fetch_report(report_id: str) -> str:
    """Fetch a report by id."""
    logger.info("Fetching report %s", report_id)
    return f"Report {report_id} is ready."

await server.sendLoggingMessage({
  level: "info",
  data: "Server started successfully",
});

MCP defines eight RFC 5424 severity levels (debug through emergency). Clients opt in to log messages per request by setting the io.modelcontextprotocol/logLevel field in the request’s _meta. Servers must not send notifications/message for requests that omit this field.

Important events to log:

• Startup steps
• Resource access
• Tool execution
• Error conditions
• Performance metrics

Common issues

The examples below use Claude Desktop’s claude_desktop_config.json; the same principles apply to any stdio-based MCP client.

Working directory

When an MCP client launches a stdio server:

• The working directory for servers launched via the client’s config may be undefined (like / on macOS) since the client 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:

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

Instead of relative paths like ./data

Environment variables

MCP servers launched over stdio inherit only a limited subset of environment variables automatically (the exact set is platform-dependent).

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

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

Server startup

Common startup problems:

1. Path Issues

   • Incorrect server executable path
   • Missing required files
   • Permission problems
   • Try using an absolute path for command

2. Configuration Errors

   • Invalid JSON syntax
   • Missing required fields
   • Type mismatches

3. Environment Problems

   • Missing environment variables
   • Incorrect variable values
   • Permission restrictions

Connection problems

When servers fail to connect:

1. Check client logs
2. Verify server process is running
3. Test standalone with Inspector
4. Verify protocol compatibility: call server/discover to see which protocol versions the server supports. An UnsupportedProtocolVersionError (-32022) lists the server’s supported versions in its data field
5. Check the per-request _meta fields: every request must carry io.modelcontextprotocol/protocolVersion and io.modelcontextprotocol/clientCapabilities, and clients should also include io.modelcontextprotocol/clientInfo. A request missing either required field is rejected with error -32602 (Invalid params), the same code returned for many other malformed inputs. If the server needs a capability the request’s clientCapabilities did not declare, such as elicitation, it returns a MissingRequiredClientCapabilityError (-32021) naming the missing capabilities. Inspect the request’s _meta and the server/discover response to verify both sides declared what you expect

Debugging in Claude Desktop

Claude Desktop is one of many MCP clients. It is available on macOS, Windows, and Linux.

Checking server status

Click the “Add files, connectors, and more” plus icon in the chat input, then hover over the Connectors menu to see connected servers and available tools.

Viewing logs

Log files are written to:

• macOS: ~/Library/Logs/Claude
• Windows: %APPDATA%\Claude\logs
• Linux: ~/.config/Claude/logs

tail -n 20 -F ~/Library/Logs/Claude/mcp*.log

tail -n 20 -F ~/.config/Claude/logs/mcp*.log

type "$env:AppData\Claude\logs\mcp*.log"

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:

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

echo '{"allowDevTools": true}' > ~/Library/Application\ Support/Claude/developer_settings.json

'{"allowDevTools": true}' | Set-Content "$env:AppData\Claude\developer_settings.json"

2. Open DevTools: Command-Option-I (macOS) or Ctrl+Alt+I (Windows)

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

Debugging workflow

Development cycle

1. Initial Development

   • Use Inspector for basic testing
   • Implement core functionality
   • Add logging points

2. Integration Testing

   • Test in your target MCP client
   • Monitor logs
   • Check error handling

Testing changes

To test changes efficiently:

• Configuration changes: Restart the MCP client
• Server code changes: Restart the client (for Claude Desktop, fully quit and reopen; closing the window is not enough)
• Quick iteration: Use Inspector during development

Best practices

Logging strategy

1. Structured Logging

   • Use consistent formats
   • Include context
   • Add timestamps
   • Track request IDs

2. Error Handling

   • Log stack traces
   • Include error context
   • Track error patterns
   • Monitor recovery

3. Performance Tracking

   • Log operation timing
   • Monitor resource usage
   • Track message sizes
   • Measure latency

Security considerations

When debugging:

1. Sensitive Data

   • Sanitize logs
   • Protect credentials
   • Mask personal information

2. Access Control

   • Verify permissions
   • Check authentication
   • Monitor access patterns

For a full treatment of MCP attack vectors and mitigations, see Security Best Practices.

Getting help

When encountering issues:

1. First Steps

   • Check server logs
   • Test with Inspector
   • Review configuration
   • Verify environment

2. Support Channels

   • GitHub issues
   • GitHub discussions

3. Providing Information

   • Log excerpts
   • Configuration files
   • Steps to reproduce
   • Environment details

Next steps

MCP Inspector

Learn to use the MCP Inspector

Build an MCP server

Walk through building a server from scratch

Connect local servers

Full claude_desktop_config.json reference and troubleshooting