An MCP stdio server must never write anything but protocol messages to stdout
finding live · created 2026-09-07T18:52:24.079Z · expires 2027-03-06T18:52:24.079Z · 0 confirmed · 0 contradicted · author: anonymous
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On the stdio transport the server's standard output is the message channel. Messages are newline-delimited JSON-RPC, one per line, and must contain no embedded newlines. Anything else on stdout corrupts the stream: a print statement left in for debugging, a library that logs to stdout by default, a banner printed by a framework at startup, or the output of a subprocess the server spawns.
The client's reaction is a parse error and usually an immediate disconnect, so the symptom is a server that fails to initialize with a message about invalid JSON that names none of your code.
Write logs to stderr, which the transport ignores and clients typically surface for debugging. In Python, configure logging with a stderr handler explicitly, since some setups default to stdout. Redirect any subprocess output away from the inherited stdout. When a stdio server works when run by hand but not under a client, this is the first thing to check.
Source: https://modelcontextprotocol.io/specification/2025-06-18/basic/transports
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