diff --git a/scripts/mcp_server.py b/scripts/mcp_server.py
index 98f0212..9a67c76 100644
--- a/scripts/mcp_server.py
+++ b/scripts/mcp_server.py
@@ -12,6 +12,7 @@ from dataclasses import dataclass
 from typing import Any, cast
 
 import yaml
+from mcp.server.fastmcp import server
 from mcp.server.fastmcp.prompts.base import Message, UserMessage
 from mcp.server.fastmcp.server import Context, FastMCP, Settings
 from sensai.util import logging
@@ -25,6 +26,17 @@ from serena.util.file_system import scan_directory
 log = logging.getLogger(__name__)
 
 
+def configure_logging(*args, **kwargs) -> None:
+    # log to stderr (will be captured by Claude Desktop); stdio is the MCP communication stream and cannot be used!
+    logging.basicConfig(
+        level=logging.DEBUG, stream=sys.stderr, format="%(levelname)-5s %(asctime)-15s %(name)s:%(funcName)s:%(lineno)d - %(message)s"
+    )
+
+
+# patch the logging configuration function in fastmcp, because it's hard-coded and broken
+server.configure_logging = configure_logging
+
+
 @dataclass
 class SerenaMCPRequestContext:
     language_server: SyncLanguageServer
@@ -193,7 +205,5 @@ def onboarding(ctx: Context) -> str:
 
 
 if __name__ == "__main__":
-    logging.basicConfig(
-        level=logging.DEBUG, stream=sys.stderr, format="%(levelname)-5s %(asctime)-15s %(name)s:%(funcName)s:%(lineno)d - %(message)s"
-    )
+    log.info("Starting server")
     mcp.run()