diff --git a/bec_widgets/cli/client_utils.py b/bec_widgets/cli/client_utils.py
index ec05ba9f..f32f73a6 100644
--- a/bec_widgets/cli/client_utils.py
+++ b/bec_widgets/cli/client_utils.py
@@ -37,6 +37,7 @@ IGNORE_WIDGETS = ["LaunchWindow"]
 PROCESS_TERMINATION_TIMEOUT = 10
 PROCESS_OUTPUT_THREAD_JOIN_TIMEOUT = 2
 PROCESS_OUTPUT_SELECT_TIMEOUT = 0.2
+GRACEFUL_SERVER_SHUTDOWN_RPC_TIMEOUT = 3
 GRACEFUL_SERVER_SHUTDOWN_TIMEOUT = 5
 OUTPUT_READER_STOP_EVENT_ATTR = "_bec_output_reader_stop_event"
 
@@ -141,19 +142,18 @@ def _terminate_plot_process(process, logger, timeout: float = PROCESS_TERMINATIO
         process.wait(timeout=timeout)
         return
     except Exception as exc:
-        logger.warning(
-            f"Failed to terminate GUI process group: {exc}; terminating process only. "
-            f"{process_details}"
-        )
+        logger.warning("Failed to terminate GUI process group; terminating process only.")
+        logger.info(f"GUI process termination failure details: {exc}. {process_details}")
         process.terminate()
 
     try:
         process.wait(timeout=timeout)
         return
     except subprocess.TimeoutExpired:
-        logger.warning(
-            f"GUI process did not stop within {timeout}s; killing it. "
-            f"{process_details}\n{_process_group_snapshot(process)}"
+        logger.warning(f"GUI process did not stop within {timeout}s; killing it.")
+        logger.info(
+            f"GUI process force-kill details: {process_details}\n"
+            f"{_process_group_snapshot(process)}"
         )
 
     try:
@@ -196,10 +196,8 @@ def _join_process_output_thread(process, thread: threading.Thread | None, logger
             logger.error(f"Failed to close stream {str(e)}")
     thread.join(timeout=PROCESS_OUTPUT_THREAD_JOIN_TIMEOUT)
     if thread.is_alive():
-        logger.warning(
-            "GUI process output reader thread did not stop after process shutdown. "
-            f"{_process_details(process)}"
-        )
+        logger.warning("GUI process output reader thread did not stop after process shutdown.")
+        logger.info(f"GUI process output reader thread details: {_process_details(process)}")
 
 
 def _start_plot_process(
@@ -630,19 +628,26 @@ class BECGuiClient(RPCBase):
         logger.info(f"Requesting graceful GUI shutdown {process_details}")
         try:
             self.launcher._run_rpc(  # pylint: disable=protected-access
-                "system.shutdown", wait_for_rpc_response=False
+                "system.shutdown",
+                wait_for_rpc_response=True,
+                timeout=GRACEFUL_SERVER_SHUTDOWN_RPC_TIMEOUT,
             )
         except Exception as exc:
             logger.warning(
-                f"Could not request graceful GUI shutdown via RPC: {exc}. " f"{process_details}"
+                "Could not confirm graceful GUI shutdown via RPC; "
+                "falling back to process termination."
             )
+            logger.info(f"Graceful GUI shutdown RPC failure details: {exc}. {process_details}")
             return False
         if _wait_for_process_exit(self._process, GRACEFUL_SERVER_SHUTDOWN_TIMEOUT):
             logger.info(f"GUI server exited after graceful shutdown {process_details}")
             return True
         logger.warning(
             "GUI server did not exit after graceful shutdown request; "
-            f"falling back to process termination. {process_details}\n"
+            "falling back to process termination."
+        )
+        logger.info(
+            f"Graceful GUI shutdown timeout details: {process_details}\n"
             f"{_process_group_snapshot(self._process)}"
         )
         return False
diff --git a/bec_widgets/utils/rpc_server.py b/bec_widgets/utils/rpc_server.py
index d3b9cf4b..a9446c68 100644
--- a/bec_widgets/utils/rpc_server.py
+++ b/bec_widgets/utils/rpc_server.py
@@ -143,6 +143,34 @@ class RPCServer:
                 f"receive_latency_s={format_elapsed(receive_latency)}"
             )
         logger.debug(f"Received RPC instruction: {msg}, metadata: {metadata}")
+
+        # Shutdown must acknowledge before teardown starts. The generic RPC path
+        # below publishes successful responses through QTimer.singleShot(0);
+        # for system.shutdown that would race with the queued app quit and
+        # dispatcher shutdown scheduled by _shutdown_gui_server().
+        if method == "system.shutdown":
+            execution_start = time.perf_counter()
+            try:
+                self.run_system_rpc(method, args, kwargs)
+            except Exception:
+                execution_duration = time.perf_counter() - execution_start
+                content = traceback.format_exc()
+                logger.error(
+                    "GUI RPC server shutdown request failed "
+                    f"request_id={request_id} method={method} gui_id={self.gui_id} "
+                    f"execution_duration_s={execution_duration:.3f}\n{content}"
+                )
+                self.send_response(request_id, False, {"error": content})
+            else:
+                execution_duration = time.perf_counter() - execution_start
+                logger.info(
+                    "GUI RPC server acknowledged shutdown request "
+                    f"request_id={request_id} method={method} gui_id={self.gui_id} "
+                    f"execution_duration_s={execution_duration:.3f}"
+                )
+                self.send_response(request_id, True, {"result": None})
+            return
+
         execution_start = time.perf_counter()
         with rpc_exception_hook(functools.partial(self.send_response, request_id, False)):
             try:
diff --git a/tests/unit_tests/test_client_utils.py b/tests/unit_tests/test_client_utils.py
index 2afdcf5b..5cf5750f 100644
--- a/tests/unit_tests/test_client_utils.py
+++ b/tests/unit_tests/test_client_utils.py
@@ -7,6 +7,7 @@ import pytest
 
 from bec_widgets.cli.client import BECDockArea
 from bec_widgets.cli.client_utils import (
+    GRACEFUL_SERVER_SHUTDOWN_RPC_TIMEOUT,
     OUTPUT_READER_STOP_EVENT_ATTR,
     BECGuiClient,
     _join_process_output_thread,
@@ -318,7 +319,9 @@ def test_client_utils_kill_server_requests_graceful_shutdown_before_signal():
         launcher_prop.return_value = launcher
         gui.kill_server()
 
-    launcher._run_rpc.assert_called_once_with("system.shutdown", wait_for_rpc_response=False)
+    launcher._run_rpc.assert_called_once_with(
+        "system.shutdown", wait_for_rpc_response=True, timeout=GRACEFUL_SERVER_SHUTDOWN_RPC_TIMEOUT
+    )
     process.wait.assert_called_once_with(timeout=5)
     killpg.assert_not_called()
     assert gui._process is None
diff --git a/tests/unit_tests/test_rpc_server.py b/tests/unit_tests/test_rpc_server.py
index 8b71d8f7..fa8ebf14 100644
--- a/tests/unit_tests/test_rpc_server.py
+++ b/tests/unit_tests/test_rpc_server.py
@@ -106,6 +106,22 @@ def test_rpc_server_system_shutdown_requests_gui_server_shutdown(rpc_server, qap
     del qapp.gui_server
 
 
+def test_on_rpc_update_system_shutdown_sends_response_before_return(rpc_server):
+    order = []
+    rpc_server.run_system_rpc = MagicMock(side_effect=lambda *_args: order.append("shutdown"))
+    rpc_server.send_response = MagicMock(side_effect=lambda *_args: order.append("response"))
+    rpc_server.serialize_result_and_send = MagicMock()
+
+    rpc_server.on_rpc_update(
+        {"action": "system.shutdown", "parameter": {"args": [], "kwargs": {}}},
+        {"request_id": "shutdown-request", "sent_at": 1.0, "deadline": 10.0, "timeout": 2},
+    )
+
+    assert order == ["shutdown", "response"]
+    rpc_server.send_response.assert_called_once_with("shutdown-request", True, {"result": None})
+    rpc_server.serialize_result_and_send.assert_not_called()
+
+
 def test_singleshot_rpc_repeat_raises_on_repeated_singleshot(rpc_server):
     """
     Test that a singleshot RPC method raises an error when called multiple times.