How to fix MCP JSON-RPC parse errors

1# Error messages you will see:
2
3# "JSON-RPC parse error (-32700)"
4# "Parse error: Unexpected token 'D' in JSON"
5# "Connection closed (-32000)"
6# "Failed to parse MCP message"
7# "Unexpected non-whitespace character after JSON"
8
9# The log might show the offending output:
10# "Received invalid data: Debug: connecting to database..."
11# This means someone wrote "Debug: connecting to database..." to stdout
12
13# Check logs:
14tail -n 30 ~/Library/Logs/Claude/mcp*.log

1// WRONG — writes to stdout, corrupts JSON-RPC stream
2console.log("Server starting...");
3console.log("Connected to database");
4console.log(`Processing request: ${id}`);
5
6// RIGHT — writes to stderr, safe for MCP
7console.error("Server starting...");
8console.error("Connected to database");
9console.error(`Processing request: ${id}`);
10
11// Also watch for:
12process.stdout.write("data"); // WRONG
13process.stderr.write("data"); // RIGHT

1import sys
2import logging
3
4# WRONG — writes to stdout
5print("Server starting...")
6print(f"Processing: {request_id}")
7
8# RIGHT — writes to stderr
9print("Server starting...", file=sys.stderr)
10print(f"Processing: {request_id}", file=sys.stderr)
11
12# BETTER — use logging module configured for stderr
13logging.basicConfig(
14    level=logging.INFO,
15    stream=sys.stderr,
16    format="%(asctime)s - %(name)s - %(levelname)s - %(message)s"
17)
18logger = logging.getLogger(__name__)
19
20logger.info("Server starting...")
21logger.info(f"Processing: {request_id}")
22logger.error("Something went wrong")

1// Node.js — redirect stdout to stderr for debugging
2// Add this at the very top of your entry file:
3const originalStdoutWrite = process.stdout.write.bind(process.stdout);
4process.stdout.write = (chunk: any, ...args: any[]) => {
5  // Log what would have gone to stdout
6  console.error(`[STDOUT INTERCEPTED]: ${chunk.toString().trim()}`);
7  // Still write it (remove this line to suppress)
8  return originalStdoutWrite(chunk, ...args);
9};
10
11# Python — redirect stdout to stderr
12import sys
13import io
14
15# Capture stdout writes
16class StderrRedirector(io.TextIOBase):
17    def write(self, s):
18        sys.stderr.write(f"[STDOUT INTERCEPTED]: {s}")
19        return len(s)
20
21sys.stdout = StderrRedirector()

1# Test with MCP Inspector
2npx -y @modelcontextprotocol/inspector
3
4# Enter your server command when prompted
5# If Inspector connects and shows tools → stdout is clean
6# If Inspector shows parse errors → stdout still has non-JSON output