MCP stdio server breaks the connection: client reports invalid JSON or the server 'closes immediately' after I added print() or console.log() debugging. Where should logs go?

Cause: With the stdio transport the client starts your server as a subprocess and the two sides exchange newline-delimited JSON-RPC messages over standard input and output. The MCP transport specification says the server must not write anything to stdout that is not a valid MCP message. A stray print(), console.log(), a library banner or a progress bar on stdout is parsed as protocol traffic, corrupts the stream and makes the client drop or fail the connection. The same rule applies the other way: the client must not send non-message data to the server's stdin. Fix (best first): 1. Send all diagnostics to stderr. The spec lets servers write UTF-8 text to stderr for logging, and the MCP debugging guide says stderr output is captured by the host application for local stdio servers. In Python use logging configured with a stderr handler, or print(..., file=sys.stderr). In Node use console.error(), not console.log(). 2. Find other stdout writers: startup banners from dependencies, deprecation notices, wrapper scripts that echo text before launching the server, and shell profile output when the command is launched through a shell. Run the server by hand and pipe its stdout through a viewer to see every byte that is not a JSON message. 3. Keep every message on a single line; the spec says messages must not contain embedded newlines. 4. Use the MCP Inspector to run the server and watch the message stream; it shows quickly which output is not valid. 5. Streamable HTTP servers do not have this stdout problem, but the guide notes that stderr is then not captured by the client, so use your own log collection there. Don't: redirect stderr into stdout to make logs visible, and don't log secrets or full tool arguments. Verify: the server connects in the client and in the Inspector, and your log lines appear in the client's MCP log or in the terminal's stderr rather than in the protocol stream. Sources: https://modelcontextprotocol.io/specification/2025-06-18/basic/transports https://modelcontextprotocol.io/docs/tools/debugging