diff --git a/src/mcp/server/mcpserver/utilities/logging.py b/src/mcp/server/mcpserver/utilities/logging.py
index 04ca38853..b1233161d 100644
--- a/src/mcp/server/mcpserver/utilities/logging.py
+++ b/src/mcp/server/mcpserver/utilities/logging.py
@@ -3,6 +3,11 @@
 import logging
 from typing import Literal
 
+# Namespace logger for all MCP SDK logging.
+# Per Python logging best practices, library code should only configure
+# its own namespace logger, never the root logger.
+_MCP_LOGGER_NAME = "mcp"
+
 
 def get_logger(name: str) -> logging.Logger:
     """Get a logger nested under MCP namespace.
@@ -21,19 +26,28 @@ def configure_logging(
 ) -> None:
     """Configure logging for MCP.
 
+    Configures only the ``mcp`` namespace logger so that application-level
+    logging configuration is not overridden.  Per the Python logging docs,
+    library code should never call ``logging.basicConfig()`` or add handlers
+    to the root logger.
+
     Args:
         level: The log level to use.
     """
-    handlers: list[logging.Handler] = []
+    mcp_logger = logging.getLogger(_MCP_LOGGER_NAME)
+    mcp_logger.setLevel(level)
+
+    # Avoid adding duplicate handlers on repeated calls.
+    if mcp_logger.handlers:
+        return
+
     try:
         from rich.console import Console
         from rich.logging import RichHandler
 
-        handlers.append(RichHandler(console=Console(stderr=True), rich_tracebacks=True))
+        handler: logging.Handler = RichHandler(console=Console(stderr=True), rich_tracebacks=True)
     except ImportError:  # pragma: no cover
-        pass
-
-    if not handlers:  # pragma: no cover
-        handlers.append(logging.StreamHandler())
+        handler = logging.StreamHandler()
+        handler.setFormatter(logging.Formatter("%(message)s"))
 
-    logging.basicConfig(level=level, format="%(message)s", handlers=handlers)
+    mcp_logger.addHandler(handler)
diff --git a/src/mcp/server/stdio.py b/src/mcp/server/stdio.py
index e526bab56..508de3438 100644
--- a/src/mcp/server/stdio.py
+++ b/src/mcp/server/stdio.py
@@ -17,6 +17,7 @@ async def run_server():
     ```
 """
 
+import os
 import sys
 from contextlib import asynccontextmanager
 from io import TextIOWrapper
@@ -38,10 +39,12 @@ async def stdio_server(stdin: anyio.AsyncFile[str] | None = None, stdout: anyio.
     # standard process handles. Encoding of stdin/stdout as text streams on
     # python is platform-dependent (Windows is particularly problematic), so we
     # re-wrap the underlying binary stream to ensure UTF-8.
+    # We duplicate the file descriptors via os.dup() to avoid closing the
+    # real sys.stdin/sys.stdout when the wrapped streams are closed.
     if not stdin:
-        stdin = anyio.wrap_file(TextIOWrapper(sys.stdin.buffer, encoding="utf-8"))
+        stdin = anyio.wrap_file(TextIOWrapper(os.fdopen(os.dup(sys.stdin.fileno()), "rb"), encoding="utf-8"))
     if not stdout:
-        stdout = anyio.wrap_file(TextIOWrapper(sys.stdout.buffer, encoding="utf-8"))
+        stdout = anyio.wrap_file(TextIOWrapper(os.fdopen(os.dup(sys.stdout.fileno()), "wb"), encoding="utf-8"))
 
     read_stream: MemoryObjectReceiveStream[SessionMessage | Exception]
     read_stream_writer: MemoryObjectSendStream[SessionMessage | Exception]