diff --git a/src/claude_agent_sdk/_internal/query.py b/src/claude_agent_sdk/_internal/query.py
index 66f10f06..f4099827 100644
--- a/src/claude_agent_sdk/_internal/query.py
+++ b/src/claude_agent_sdk/_internal/query.py
@@ -922,7 +922,7 @@ async def wait_for_result_and_end_input(self) -> None:
         follow-up turn, which ends in such a result), or in _read_messages'
         finally block if the process exits early.
         """
-        if self.sdk_mcp_servers or self.hooks:
+        if self.sdk_mcp_servers or self.hooks or self.can_use_tool:
             logger.debug(
                 "Waiting for a run-ending result before closing stdin "
                 f"(sdk_mcp_servers={len(self.sdk_mcp_servers)}, "