Troubleshooting for the Snyk MCP server

If you encounter issues with the Snyk MCP server or its integration, try the troubleshooting steps provided here.

Check Snyk CLI version compatibility

After downloading or updating the CLI, run snyk version. The version must be higher than or equal to v1.1296.2.

Snyk recommends using the latest version.

Verify Snyk CLI path and permissions

If you have specified a direct path to the snyk executable in your mcpconfig.json , verify that the path is correct.

Ensure the Snyk CLI binary has execute permissions.

Basic repository scanning (crucial diagnostic)

Basic repository scanning is a key step for many issues. Before suspecting complex MCP integration problems, confirm that the Snyk CLI you are using to run the MCP server can scan your repository directly from your terminal.

Navigate to the root directory of your Project and run:

• /path/to/your/snykCli test - for open-source vulnerabilities

• /path/to/your/snykCli code test - for code issues

If these direct scans fail, resolve those issues first, for example, authentication, Organization settings, and Snyk Code enablement for your Organization, then initiate a new scan.

Authentication issues

• Some MCP hosts (the client application integrating the Snyk MCP server) might restrict MCP server processes, which can interfere with the Snyk authentication flow, for example, browser-based login.

• Mitigation strategies

  • Try starting the Snyk MCP server in sse transport mode instead of stdio: snyk mcp -t sse and set the URL in your mcpconfig.json file.

  • Provide a Snyk authentication token directly using the SNYK_TOKEN environment variable.

Some MCP hosts, such as the client application integrating with the Snyk MCP server, can restrict MCP server processes, which can interfere with the Snyk authentication flow, for example, browser-based login.

Use these mitigation strategies to resolve the issue:

• Start the Snyk MCP server in sse transport mode instead of stdio: snyk mcp -t sse --experimental and set the URL in your mcpconfig.json file.

• Authenticate with Snyk by supplying your authentication token through the SNYK_TOKEN=<TOKEN> environment variable. To obtain your token, generate a Snyk Personal Access Token or retrieve your Snyk API Token directly from the Snyk web interface. For details on Personal Access Token, see Authentication for API, for details on Snyk API Token, see Obtain and use your Snyk API token.

Snyk Organization configuration

If your Snyk account is part of multiple Organizations, or if scans are not appearing in the expected place, ensure the correct Snyk Organization is configured. You can set this using:

• The command snyk config set org=<YOUR_ORG_ID>

• The environment variable SNYK_CFG_ORG=<YOUR_ORG_ID>

Environment variable propagation

Verify that the necessary environment variables, for example, SNYK_TOKEN, SNYK_CFG_ORG, and proxy settings, are correctly propagated to the Snyk MCP server process.

Proxy configuration

If you are behind a corporate proxy, ensure that the http_proxy and https_proxy environment variables are correctly set and accessible to the Snyk CLI and MCP server process.

SSE Transport specifics

If you are using SSE through the snyk mcp -t sse command, then check if the local firewall is blocking incoming connections to the port used by the Snyk MCP SSE server.

Folder Trust

if you are experiencing issues related to folder trust, you can disable this feature by using the

--disable-trust CLI flag.

Remember that the MCP server can only be run locally when using SSE transport.

Verbose logging and debugging

Use these suggestions to improve and expand on your Snyk CLI debug output to troubleshoot MCP-related issues:

• For more detailed Snyk CLI logs, which are useful whether you are starting the snyk mcp server or performing direct test scans (see Basic repository scanning), you can add verbosity parameters to your Snyk commands. These include using the -d or --debug flag for debug level output, for example:

  • snyk mcp -t sse -d

  • snyk test -d

  • snyk code test -d

• For even more granular, trace-level logging, you can use the --log-level=trace option or set the SNYK_LOG_LEVEL=trace environment variable:

  • snyk mcp -t sse -d --log-level=trace

  • SNYK_LOG_LEVEL=trace snyk mcp -t sse -d

• Inspect the MCP client and host logs from your AI tool, IDE, or MCP client application. These logs might contain errors related to connecting to or communicating with the Snyk MCP server.

Add verbosity parameters to your Snyk commands to obtain more detailed Snyk CLI logs, which are helpful when starting the server or running direct test scans (refer to Basic repository scanning). These include using the -d or --debug flag for debug level output, for example:

• snyk mcp -t sse -d

• snyk test -d

• snyk code test -d

• For even more granular, trace-level logging, you can use the --log-level=trace option or set the SNYK_LOG_LEVEL=trace environment variable:

  • snyk mcp -t sse -d --log-level=trace

  • SNYK_LOG_LEVEL=trace snyk mcp -t sse -d

Inspect the MCP client and host logs from your AI tool, IDE, or MCP client application. These logs can contain errors related to connecting to or communicating with the Snyk MCP server.