diff --git a/bec_widgets/applications/companion_app.py b/bec_widgets/applications/companion_app.py
index 05944463e..43524194a 100644
--- a/bec_widgets/applications/companion_app.py
+++ b/bec_widgets/applications/companion_app.py
@@ -5,6 +5,7 @@
 import os
 import signal
 import sys
+import traceback
 from contextlib import redirect_stderr, redirect_stdout
 
 import darkdetect
@@ -63,6 +64,7 @@ def __init__(self, args):
         self.app: QApplication | None = None
         self.launcher_window: LaunchWindow | None = None
         self.dispatcher: BECDispatcher | None = None
+        self._shutdown_started = False
 
     def start(self):
         """
@@ -74,6 +76,7 @@ def start(self):
             bec_logger._stderr_log_level = bec_logger.LOGLEVEL.ERROR
             bec_logger._update_sinks()
 
+        bec_logger.disabled_modules = ["bec_lib.scan_items"]
         with redirect_stdout(SimpleFileLikeFromLogOutputFunc(logger.info)):  # type: ignore
             with redirect_stderr(SimpleFileLikeFromLogOutputFunc(logger.error)):  # type: ignore
                 self._run()
@@ -122,17 +125,8 @@ def _run(self):
         self.app.aboutToQuit.connect(self.shutdown)
         self.app.setQuitOnLastWindowClosed(True)
 
-        def sigint_handler(*args):
-            # display message, for people to let it terminate gracefully
-            print("Caught SIGINT, exiting")
-            # Widgets should be all closed.
-            with RPCRegister.delayed_broadcast():
-                for widget in QApplication.instance().topLevelWidgets():  # type: ignore
-                    widget.close()
-            self.shutdown()
-
-        signal.signal(signal.SIGINT, sigint_handler)
-        signal.signal(signal.SIGTERM, sigint_handler)
+        signal.signal(signal.SIGINT, self.request_shutdown)
+        signal.signal(signal.SIGTERM, self.request_shutdown)
 
         sys.exit(self.app.exec())
 
@@ -149,16 +143,67 @@ def setup_bec_icon(self):
         )
         self.app.setWindowIcon(icon)
 
+    def request_shutdown(self, signum=None, _frame=None):
+        """
+        Request Qt application shutdown from an RPC call or OS signal.
+
+        Cleanup itself is handled by ``shutdown()``, which is connected to
+        ``QApplication.aboutToQuit``. Calling it directly here would run BEC/RPC
+        teardown before Qt has processed the widget close events.
+        """
+        signal_name = signal.Signals(signum).name if signum is not None else "shutdown"
+        pid = os.getpid()
+        if self.app is None:
+            logger.info(f"Caught {signal_name}, shutting down GUI server pid={pid} without app")
+            self.shutdown()
+            return
+
+        widgets = [
+            f"{widget.__class__.__name__}(objectName={widget.objectName()!r})"
+            for widget in self.app.topLevelWidgets()
+        ]
+        logger.info(
+            f"Caught {signal_name}, requesting GUI server shutdown pid={pid} "
+            f"top_level_widgets={widgets}"
+        )
+        with RPCRegister.delayed_broadcast():
+            for widget in self.app.topLevelWidgets():
+                widget.close()
+        self.app.quit()
+
+    @staticmethod
+    def _run_shutdown_step(step: str, callback):
+        try:
+            callback()
+        except Exception as exc:
+            logger.error(
+                f"GUIServer shutdown step failed pid={os.getpid()} step={step}: {exc}\n"
+                f"{traceback.format_exc()}"
+            )
+
     def shutdown(self):
-        logger.info("Shutdown GUIServer", repr(self))
-        if self.launcher_window and shiboken6.isValid(self.launcher_window):
-            self.launcher_window.close()
-            self.launcher_window.deleteLater()
-        if pylsp_server.is_running():
-            pylsp_server.stop()
-        if self.dispatcher:
-            self.dispatcher.stop_cli_server()
-            self.dispatcher.disconnect_all()
+        if self._shutdown_started:
+            return
+        self._shutdown_started = True
+        logger.info(f"Shutdown GUIServer pid={os.getpid()} {repr(self)}")
+
+        def close_launcher_window():
+            if self.launcher_window and shiboken6.isValid(self.launcher_window):
+                self.launcher_window.close()
+                self.launcher_window.deleteLater()
+
+        def stop_pylsp_server():
+            if pylsp_server.is_running():
+                pylsp_server.stop()
+
+        def stop_dispatcher():
+            if self.dispatcher:
+                self.dispatcher.stop_cli_server()
+                self.dispatcher.disconnect_all()
+
+        self._run_shutdown_step("close_launcher_window", close_launcher_window)
+        self._run_shutdown_step("stop_pylsp_server", stop_pylsp_server)
+        self._run_shutdown_step("stop_dispatcher", stop_dispatcher)
 
 
 def main():
diff --git a/bec_widgets/applications/launch_window.py b/bec_widgets/applications/launch_window.py
index 4eae81a48..50f8e3b1b 100644
--- a/bec_widgets/applications/launch_window.py
+++ b/bec_widgets/applications/launch_window.py
@@ -660,20 +660,35 @@ def _launcher_is_last_widget(self, connections: dict) -> bool:
         Check if the launcher is the last widget in the application.
         """
 
-        # get all parents of connections
         for connection in connections.values():
-            try:
-                parent = connection.parent()
-                if parent is None and connection.objectName() != self.objectName():
-                    logger.info(
-                        f"Found non-launcher connection without parent: {connection.objectName()}"
-                    )
-                    return False
-            except Exception as e:
-                logger.error(f"Error getting parent of connection: {e}")
+            if not self._connection_belongs_to_launcher(connection):
                 return False
         return True
 
+    def _connection_belongs_to_launcher(self, connection: QObject) -> bool:
+        """
+        Check whether a registered connection is the launcher itself or part of its Qt hierarchy.
+
+        Registered top-level windows such as BECMainWindowNoRPC are expected when another GUI is
+        open. They are not launcher children, but they are also not an error condition.
+        """
+        try:
+            if connection is self or getattr(connection, "gui_id", None) == self.gui_id:
+                return True
+            if connection.objectName() == self.objectName():
+                return True
+
+            parent = connection.parent()
+            while parent is not None:
+                if parent is self:
+                    return True
+                parent = parent.parent()
+        except Exception as e:
+            logger.error(f"Error checking launcher ownership of connection: {e}")
+            return False
+
+        return False
+
     def _turn_off_the_lights(self, connections: dict):
         """
         If there is only one connection remaining, it is the launcher, so we show it.
diff --git a/bec_widgets/cli/client_utils.py b/bec_widgets/cli/client_utils.py
index 21276773a..f32f73a6a 100644
--- a/bec_widgets/cli/client_utils.py
+++ b/bec_widgets/cli/client_utils.py
@@ -5,6 +5,7 @@
 import json
 import os
 import select
+import signal
 import subprocess
 import threading
 import time
@@ -33,6 +34,12 @@
 logger = bec_logger.logger
 
 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"
 
 RegistryState: TypeAlias = dict[
     Literal["gui_id", "name", "widget_class", "config", "__rpc__", "container_proxy"],
@@ -53,14 +60,16 @@ def _filter_output(output: str) -> str:
     return output
 
 
-def _get_output(process, logger) -> None:
+def _get_output(process, logger, stop_event: threading.Event | None = None) -> None:
     log_func = {process.stdout: logger.debug, process.stderr: logger.info}
     stream_buffer = {process.stdout: [], process.stderr: []}
     try:
         os.set_blocking(process.stdout.fileno(), False)
         os.set_blocking(process.stderr.fileno(), False)
-        while process.poll() is None:
-            readylist, _, _ = select.select([process.stdout, process.stderr], [], [], 1)
+        while process.poll() is None and not (stop_event and stop_event.is_set()):
+            readylist, _, _ = select.select(
+                [process.stdout, process.stderr], [], [], PROCESS_OUTPUT_SELECT_TIMEOUT
+            )
             for stream in (process.stdout, process.stderr):
                 buf = stream_buffer[stream]
                 if stream in readylist:
@@ -75,6 +84,122 @@ def _get_output(process, logger) -> None:
         logger.error(f"Error reading process output: {str(e)}")
 
 
+def _process_group_id(process) -> int | None:
+    pid = getattr(process, "pid", None)
+    if os.name != "posix" or not isinstance(pid, int):
+        return None
+    try:
+        return os.getpgid(pid)
+    except ProcessLookupError:
+        return None
+
+
+def _process_details(process) -> str:
+    args = getattr(process, "args", None)
+    if isinstance(args, list):
+        command = " ".join(str(arg) for arg in args)
+    else:
+        command = str(args)
+    return (
+        f"pid={getattr(process, 'pid', None)} pgid={_process_group_id(process)} command={command}"
+    )
+
+
+def _process_group_snapshot(process) -> str:
+    pgid = _process_group_id(process)
+    if pgid is None:
+        return "Process group snapshot unavailable: process group no longer exists"
+    try:
+        result = subprocess.run(
+            ["ps", "-o", "pid,ppid,pgid,stat,command", "-g", str(pgid)],
+            check=False,
+            capture_output=True,
+            text=True,
+            timeout=2,
+        )
+    except Exception as exc:
+        return f"Process group snapshot unavailable: {exc}"
+    output = result.stdout.strip()
+    if not output:
+        return f"Process group snapshot empty for pgid={pgid}"
+    return output
+
+
+def _terminate_plot_process(process, logger, timeout: float = PROCESS_TERMINATION_TIMEOUT) -> None:
+    if process.poll() is not None:
+        return
+
+    process_details = _process_details(process)
+    try:
+        pgid = _process_group_id(process)
+        if pgid is not None:
+            logger.info(f"Terminating GUI process group {process_details}")
+            os.killpg(pgid, signal.SIGTERM)
+        else:
+            logger.info(f"Terminating GUI process {process_details}")
+            process.terminate()
+    except ProcessLookupError:
+        process.wait(timeout=timeout)
+        return
+    except Exception as exc:
+        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.")
+        logger.info(
+            f"GUI process force-kill details: {process_details}\n"
+            f"{_process_group_snapshot(process)}"
+        )
+
+    try:
+        pgid = _process_group_id(process)
+        if pgid is not None:
+            os.killpg(pgid, signal.SIGKILL)
+        else:
+            process.kill()
+    except ProcessLookupError as e:
+        logger.error(f"Failed to kill GUI process group: {e}")
+        process.wait(timeout=timeout)
+        return
+    process.wait(timeout=timeout)
+
+
+def _wait_for_process_exit(process, timeout: float) -> bool:
+    try:
+        process.wait(timeout=timeout)
+    except subprocess.TimeoutExpired:
+        return False
+    return True
+
+
+def _join_process_output_thread(process, thread: threading.Thread | None, logger) -> None:
+    if thread is None:
+        return
+    thread.join(timeout=PROCESS_OUTPUT_THREAD_JOIN_TIMEOUT)
+    if not thread.is_alive():
+        return
+
+    if stop_event := getattr(thread, OUTPUT_READER_STOP_EVENT_ATTR, None):
+        stop_event.set()
+
+    for stream in (process.stdout, process.stderr):
+        if stream is None:
+            continue
+        try:
+            stream.close()
+        except OSError as e:
+            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.")
+        logger.info(f"GUI process output reader thread details: {_process_details(process)}")
+
+
 def _start_plot_process(
     gui_id: str,
     gui_class_id: str,
@@ -126,8 +251,14 @@ def _start_plot_process(
     if logger is None:
         process_output_processing_thread = None
     else:
+        process_output_stop_event = threading.Event()
         process_output_processing_thread = threading.Thread(
-            target=_get_output, args=(process, logger)
+            target=_get_output, args=(process, logger, process_output_stop_event)
+        )
+        setattr(
+            process_output_processing_thread,
+            OUTPUT_READER_STOP_EVENT_ATTR,
+            process_output_stop_event,
         )
         process_output_processing_thread.start()
     return process, process_output_processing_thread
@@ -222,7 +353,7 @@ def __init__(self, **kwargs) -> None:
         self._ipython_registry: dict[str, RPCReference] = {}
         self.available_widgets = AvailableWidgetsNamespace()
         register_serializer_extension()
-        self._rpc_timeout = 5
+        self._rpc_timeout = 60
 
     ####################
     #### Client API ####
@@ -465,11 +596,13 @@ def kill_server(self) -> None:
 
         if self._process:
             logger.success("Stopping GUI...")
-            self._process.terminate()
-            if self._process_output_processing_thread:
-                self._process_output_processing_thread.join()
-            self._process.wait()
+            if not self._request_server_shutdown():
+                _terminate_plot_process(self._process, logger)
+            _join_process_output_thread(
+                self._process, self._process_output_processing_thread, logger
+            )
             self._process = None
+            self._process_output_processing_thread = None
 
         # Unregister the registry state
         self._client.connector.unregister(
@@ -488,6 +621,37 @@ def close(self):
     #### Private methods ####
     #########################
 
+    def _request_server_shutdown(self) -> bool:
+        if self._process is None or self._process.poll() is not None:
+            return True
+        process_details = _process_details(self._process)
+        logger.info(f"Requesting graceful GUI shutdown {process_details}")
+        try:
+            self.launcher._run_rpc(  # pylint: disable=protected-access
+                "system.shutdown",
+                wait_for_rpc_response=True,
+                timeout=GRACEFUL_SERVER_SHUTDOWN_RPC_TIMEOUT,
+            )
+        except Exception as exc:
+            logger.warning(
+                "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; "
+            "falling back to process termination."
+        )
+        logger.info(
+            f"Graceful GUI shutdown timeout details: {process_details}\n"
+            f"{_process_group_snapshot(self._process)}"
+        )
+        return False
+
     def _check_if_server_is_alive(self):
         """Checks if the process is alive"""
         if self._process is None:
diff --git a/bec_widgets/cli/rpc/rpc_base.py b/bec_widgets/cli/rpc/rpc_base.py
index 2523789e1..a5061ae48 100644
--- a/bec_widgets/cli/rpc/rpc_base.py
+++ b/bec_widgets/cli/rpc/rpc_base.py
@@ -2,6 +2,7 @@
 
 import inspect
 import threading
+import time
 import uuid
 from functools import wraps
 from typing import TYPE_CHECKING, Any, cast
@@ -9,6 +10,7 @@
 from bec_lib.client import BECClient
 from bec_lib.device import DeviceBaseWithConfig
 from bec_lib.endpoints import MessageEndpoints
+from bec_lib.logger import bec_logger
 from bec_lib.utils.import_utils import lazy_import, lazy_import_from
 
 if TYPE_CHECKING:  # pragma: no cover
@@ -25,6 +27,7 @@
 # pylint: disable=protected-access
 
 _DEFAULT_RPC_TIMEOUT = object()
+logger = bec_logger.logger
 
 
 def _name_arg(arg):
@@ -261,12 +264,39 @@ def _run_rpc(
                 MessageEndpoints.gui_instruction_response(request_id), cb=self._on_rpc_response
             )
 
+        target_gui_id = gui_id or self._gui_id
+        sent_at = time.time()
+        deadline = sent_at + timeout if timeout is not None else None
+        rpc_msg.metadata.update(
+            {
+                "method": method,
+                "receiver": receiver,
+                "target_gui_id": target_gui_id,
+                "object_name": self.object_name,
+                "wait_for_response": wait_for_rpc_response,
+                "timeout": timeout,
+                "sent_at": sent_at,
+                "deadline": deadline,
+            }
+        )
+        logger.info(
+            "Sending GUI RPC request "
+            f"request_id={request_id} method={method} receiver={receiver} "
+            f"target_gui_id={target_gui_id} object_name={self.object_name} "
+            f"wait_for_response={wait_for_rpc_response} timeout={timeout}"
+        )
         self._client.connector.set_and_publish(MessageEndpoints.gui_instructions(receiver), rpc_msg)
 
         if wait_for_rpc_response:
             try:
                 finished = self._msg_wait_event.wait(timeout)
                 if not finished:
+                    logger.error(
+                        "GUI RPC response timeout "
+                        f"request_id={request_id} method={method} receiver={receiver} "
+                        f"target_gui_id={target_gui_id} object_name={self.object_name} "
+                        f"timeout={timeout}"
+                    )
                     raise RPCResponseTimeoutError(request_id, timeout)
             finally:
                 self._msg_wait_event.clear()
@@ -278,6 +308,12 @@ def _run_rpc(
             # the _on_rpc_response method
             assert isinstance(self._rpc_response, messages.RequestResponseMessage)
 
+            logger.info(
+                "Received GUI RPC response "
+                f"request_id={request_id} method={method} receiver={receiver} "
+                f"target_gui_id={target_gui_id} object_name={self.object_name} "
+                f"accepted={self._rpc_response.accepted}"
+            )
             if not self._rpc_response.accepted:
                 raise ValueError(self._rpc_response.message["error"])
             msg_result = self._rpc_response.message.get("result")
@@ -286,6 +322,7 @@ def _run_rpc(
 
     def _on_rpc_response(self, msg_obj: MessageObject) -> None:
         msg = cast(messages.RequestResponseMessage, msg_obj.value)
+        logger.debug(f"GUI RPC response callback received: {msg}")
         self._rpc_response = msg
         self._msg_wait_event.set()
 
diff --git a/bec_widgets/utils/bec_dispatcher.py b/bec_widgets/utils/bec_dispatcher.py
index af739ef27..6f1453155 100644
--- a/bec_widgets/utils/bec_dispatcher.py
+++ b/bec_widgets/utils/bec_dispatcher.py
@@ -3,8 +3,9 @@
 import collections
 import random
 import string
+import time
 from collections.abc import Callable
-from typing import TYPE_CHECKING, DefaultDict, Hashable, Union
+from typing import TYPE_CHECKING, Any, DefaultDict, Hashable, Union
 
 import louie
 import redis
@@ -15,6 +16,7 @@
 from qtpy.QtCore import QObject
 from qtpy.QtCore import Signal as pyqtSignal
 
+from bec_widgets.utils.rpc_logging import elapsed_seconds, format_elapsed
 from bec_widgets.utils.serialization import register_serializer_extension
 
 logger = bec_logger.logger
@@ -25,6 +27,39 @@
     from bec_widgets.utils.rpc_server import RPCServer
 
 
+def _log_rpc_dispatcher_receive(msg_content: Any, metadata: Any) -> None:
+    if not isinstance(msg_content, dict) or not isinstance(metadata, dict):
+        return
+    request_id = metadata.get("request_id")
+    method = msg_content.get("action")
+    parameter = msg_content.get("parameter")
+    if request_id is None or method is None or not isinstance(parameter, dict):
+        return
+
+    dispatch_received_at = time.time()
+    sent_at = metadata.get("sent_at")
+    deadline = metadata.get("deadline")
+    timeout = metadata.get("timeout")
+    dispatch_latency = elapsed_seconds(sent_at, dispatch_received_at)
+    stale_on_dispatch = deadline is not None and dispatch_received_at > deadline
+    target_gui_id = parameter.get("gui_id") or metadata.get("target_gui_id")
+
+    logger.info(
+        "GUI RPC dispatcher received request before Qt callback emit "
+        f"request_id={request_id} method={method} receiver={metadata.get('receiver')} "
+        f"target_gui_id={target_gui_id} object_name={metadata.get('object_name')} "
+        f"timeout={timeout} dispatch_latency_s={format_elapsed(dispatch_latency)} "
+        f"stale_on_dispatch={stale_on_dispatch}"
+    )
+    if stale_on_dispatch:
+        logger.warning(
+            "GUI RPC dispatcher received request after client timeout deadline "
+            f"request_id={request_id} method={method} receiver={metadata.get('receiver')} "
+            f"target_gui_id={target_gui_id} object_name={metadata.get('object_name')} "
+            f"timeout={timeout} dispatch_latency_s={format_elapsed(dispatch_latency)}"
+        )
+
+
 class QtThreadSafeCallback(QObject):
     """QtThreadSafeCallback is a wrapper around a callback function to make it thread-safe for Qt."""
 
@@ -88,10 +123,12 @@ def _execute_callback(self, cb, msg, kwargs):
 
             # we can notice kwargs are lost when passed to Qt slot
             metadata = msg.metadata
+            _log_rpc_dispatcher_receive(msg.content, metadata)
             cb(msg.content, metadata)
         else:
             # from stream
             msg = msg["data"]
+            _log_rpc_dispatcher_receive(msg.content, msg.metadata)
             cb(msg.content, msg.metadata)
 
 
diff --git a/bec_widgets/utils/rpc_logging.py b/bec_widgets/utils/rpc_logging.py
new file mode 100644
index 000000000..9ef28b2db
--- /dev/null
+++ b/bec_widgets/utils/rpc_logging.py
@@ -0,0 +1,16 @@
+from __future__ import annotations
+
+
+def elapsed_seconds(start: float | int | None, stop: float) -> float | None:
+    if start is None:
+        return None
+    try:
+        return max(0.0, stop - float(start))
+    except (TypeError, ValueError):
+        return None
+
+
+def format_elapsed(elapsed: float | None) -> str:
+    if elapsed is None:
+        return "unknown"
+    return f"{elapsed:.3f}"
diff --git a/bec_widgets/utils/rpc_server.py b/bec_widgets/utils/rpc_server.py
index 25fd0cca2..a9446c680 100644
--- a/bec_widgets/utils/rpc_server.py
+++ b/bec_widgets/utils/rpc_server.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import functools
+import time
 import traceback
 import types
 from contextlib import contextmanager
@@ -11,13 +12,14 @@
 from bec_lib.logger import bec_logger
 from bec_lib.utils.import_utils import lazy_import
 from qtpy.QtCore import Qt, QTimer
-from qtpy.QtWidgets import QWidget
+from qtpy.QtWidgets import QApplication, QWidget
 from redis.exceptions import RedisError
 
 from bec_widgets.utils.bec_connector import BECConnector
 from bec_widgets.utils.bec_dispatcher import BECDispatcher
 from bec_widgets.utils.container_utils import WidgetContainerUtils
 from bec_widgets.utils.error_popups import ErrorPopupUtility
+from bec_widgets.utils.rpc_logging import elapsed_seconds, format_elapsed
 from bec_widgets.utils.rpc_register import RPCRegister
 from bec_widgets.utils.screen_utils import apply_window_geometry
 from bec_widgets.widgets.containers.dock_area.dock_area import BECDockArea
@@ -115,27 +117,107 @@ def on_rpc_update(self, msg: dict, metadata: dict):
         if request_id is None:
             logger.error("Received RPC instruction without request_id")
             return
+        method = msg.get("action")
+        parameter = msg.get("parameter", {})
+        args = parameter.get("args", [])
+        kwargs = parameter.get("kwargs", {})
+        target_gui_id = parameter.get("gui_id")
+        sent_at = metadata.get("sent_at")
+        deadline = metadata.get("deadline")
+        timeout = metadata.get("timeout")
+        received_at = time.time()
+        receive_latency = elapsed_seconds(sent_at, received_at)
+        stale_on_receive = deadline is not None and received_at > deadline
+        logger.info(
+            "GUI RPC server received request "
+            f"request_id={request_id} method={method} gui_id={self.gui_id} "
+            f"target_gui_id={target_gui_id} timeout={timeout} "
+            f"receive_latency_s={format_elapsed(receive_latency)} "
+            f"stale_on_receive={stale_on_receive}"
+        )
+        if stale_on_receive:
+            logger.warning(
+                "GUI RPC server received request after client timeout deadline "
+                f"request_id={request_id} method={method} gui_id={self.gui_id} "
+                f"target_gui_id={target_gui_id} timeout={timeout} "
+                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:
-                method = msg["action"]
-                args = msg["parameter"].get("args", [])
-                kwargs = msg["parameter"].get("kwargs", {})
                 if method.startswith("system."):
                     res = self.run_system_rpc(method, args, kwargs)
                 else:
-                    obj = self.get_object_from_config(msg["parameter"])
+                    obj = self.get_object_from_config(parameter)
                     res = self.run_rpc(obj, method, args, kwargs)
             except Exception:
+                execution_duration = time.perf_counter() - execution_start
                 content = traceback.format_exc()
-                logger.error(f"Error while executing RPC instruction: {content}")
+                logger.error(
+                    "GUI RPC server execution failed "
+                    f"request_id={request_id} method={method} gui_id={self.gui_id} "
+                    f"target_gui_id={target_gui_id} execution_duration_s={execution_duration:.3f}\n"
+                    f"{content}"
+                )
                 self.send_response(request_id, False, {"error": content})
             else:
+                execution_duration = time.perf_counter() - execution_start
+                response_stale = deadline is not None and time.time() > deadline
+                logger.info(
+                    "GUI RPC server executed request "
+                    f"request_id={request_id} method={method} gui_id={self.gui_id} "
+                    f"target_gui_id={target_gui_id} execution_duration_s={execution_duration:.3f} "
+                    f"response_after_client_deadline={response_stale}"
+                )
+                if response_stale:
+                    logger.warning(
+                        "GUI RPC server response is late for client timeout "
+                        f"request_id={request_id} method={method} gui_id={self.gui_id} "
+                        f"target_gui_id={target_gui_id} timeout={timeout} "
+                        f"execution_duration_s={execution_duration:.3f}"
+                    )
                 logger.debug(f"RPC instruction executed successfully: {res}")
                 self._rpc_singleshot_repeats[request_id] = SingleshotRPCRepeat()
                 QTimer.singleShot(0, lambda: self.serialize_result_and_send(request_id, res))
 
     def send_response(self, request_id: str, accepted: bool, msg: dict):
+        log_message = (
+            "GUI RPC server publishing response "
+            f"request_id={request_id} gui_id={self.gui_id} accepted={accepted}"
+        )
+        if accepted:
+            logger.info(log_message)
+        else:
+            logger.error(log_message)
         self.client.connector.set_and_publish(
             MessageEndpoints.gui_instruction_response(request_id),
             messages.RequestResponseMessage(accepted=accepted, message=msg),
@@ -236,10 +318,23 @@ def _resolve_rpc_target(self, obj, method: str) -> tuple[object, object]:
     def run_system_rpc(self, method: str, args: list, kwargs: dict):
         if method == "system.launch_dock_area":
             return self._launch_dock_area(*args, **kwargs)
+        if method == "system.shutdown":
+            return self._shutdown_gui_server()
         if method == "system.list_capabilities":
-            return {"system.launch_dock_area": True}
+            return {"system.launch_dock_area": True, "system.shutdown": True}
         raise ValueError(f"Unknown system RPC method: {method}")
 
+    @staticmethod
+    def _shutdown_gui_server() -> None:
+        app = QApplication.instance()
+        if app is None:
+            return
+        gui_server = getattr(app, "gui_server", None)
+        if gui_server is not None and hasattr(gui_server, "request_shutdown"):
+            QTimer.singleShot(0, gui_server.request_shutdown)
+            return
+        QTimer.singleShot(0, app.quit)
+
     @staticmethod
     def _launch_dock_area(
         name: str | None = None,
@@ -297,7 +392,14 @@ def serialize_result_and_send(self, request_id: str, res: object):
                 res = self.serialize_object(res)
         except RegistryNotReadyError:
             try:
-                self._rpc_singleshot_repeats[request_id] += retry_delay
+                repeat = self._rpc_singleshot_repeats[request_id]
+                repeat += retry_delay
+                logger.warning(
+                    "GUI RPC result serialization delayed; retrying "
+                    f"request_id={request_id} retry_delay_ms={retry_delay} "
+                    f"accumulated_delay_ms={repeat.accumulated_delay} "
+                    f"max_delay_ms={repeat.max_delay}"
+                )
                 QTimer.singleShot(
                     retry_delay, lambda: self.serialize_result_and_send(request_id, res)
                 )
@@ -407,8 +509,9 @@ def _serialize_bec_connector(self, connector: BECConnector, wait=False) -> dict:
                 container_proxy = parent.gui_id
             else:
                 container_proxy = None
-        except Exception:
+        except Exception as e:
             container_proxy = None
+            logger.error(f"Error while serializing RPC result: {e}")
 
         if wait and not self.rpc_register.object_is_registered(connector):
             raise RegistryNotReadyError(f"Connector {connector} not registered yet")
diff --git a/bec_widgets/widgets/control/buttons/button_abort/button_abort.py b/bec_widgets/widgets/control/buttons/button_abort/button_abort.py
index 4a9585dc2..c17675020 100644
--- a/bec_widgets/widgets/control/buttons/button_abort/button_abort.py
+++ b/bec_widgets/widgets/control/buttons/button_abort/button_abort.py
@@ -1,3 +1,4 @@
+from bec_lib.logger import bec_logger
 from bec_qthemes import material_icon
 from qtpy.QtCore import Qt
 from qtpy.QtWidgets import QHBoxLayout, QPushButton, QToolButton, QWidget
@@ -5,6 +6,8 @@
 from bec_widgets.utils.bec_widget import BECWidget
 from bec_widgets.utils.error_popups import SafeSlot
 
+logger = bec_logger.logger
+
 
 class AbortButton(BECWidget, QWidget):
     """A button that abort the scan."""
@@ -55,7 +58,7 @@ def abort_scan(
             scan_id(str|None): The scan id to abort. If None, the current scan will be aborted.
         """
         if self.scan_id is not None:
-            print(f"Aborting scan with scan_id: {self.scan_id}")
+            logger.info(f"Aborting scan with scan_id: {self.scan_id}")
             self.queue.request_scan_abortion(scan_id=self.scan_id)
         else:
             self.queue.request_scan_abortion()
diff --git a/bec_widgets/widgets/plots/image/image_base.py b/bec_widgets/widgets/plots/image/image_base.py
index 57bbf95c5..db8e783e4 100644
--- a/bec_widgets/widgets/plots/image/image_base.py
+++ b/bec_widgets/widgets/plots/image/image_base.py
@@ -460,7 +460,7 @@ def enable_colorbar(
                 self._color_bar = None
 
             def disable_autorange():
-                print("Disabling autorange")
+                logger.info("Disabling autorange")
                 self.setProperty("autorange", False)
 
             if style == "simple":
@@ -928,7 +928,7 @@ def _set_autorange(self, enabled: bool, sync: bool = True):
                 # if sync:
                 self._sync_colorbar_levels()
         self._sync_autorange_switch()
-        print(f"Autorange set to {enabled}")
+        logger.info(f"Autorange set to {enabled}")
 
     @SafeProperty(str)
     def autorange_mode(self) -> str:
diff --git a/bec_widgets/widgets/plots/waveform/waveform.py b/bec_widgets/widgets/plots/waveform/waveform.py
index 467a6138a..35a2873ba 100644
--- a/bec_widgets/widgets/plots/waveform/waveform.py
+++ b/bec_widgets/widgets/plots/waveform/waveform.py
@@ -2449,7 +2449,7 @@ def _check_dataset_size_and_confirm(self, dataset_obj, device_entry: str) -> boo
                 first_key = next(iter(info))
                 mem_bytes = info[first_key]["value"]["mem_size"]
             size_mb = mem_bytes / (1024 * 1024)
-            print(f"Dataset size: {size_mb:.1f} MB")
+            logger.info(f"Dataset size: {size_mb:.1f} MB")
         except Exception as exc:  # noqa: BLE001
             logger.error(f"Unable to evaluate dataset size: {exc}")
             return True
diff --git a/bec_widgets/widgets/progress/scan_progressbar/scan_progressbar.py b/bec_widgets/widgets/progress/scan_progressbar/scan_progressbar.py
index 392fecb81..c10f7b3b1 100644
--- a/bec_widgets/widgets/progress/scan_progressbar/scan_progressbar.py
+++ b/bec_widgets/widgets/progress/scan_progressbar/scan_progressbar.py
@@ -155,7 +155,6 @@ def __init__(
         self._progress_device = None
         self.task = None
         self.scan_number = None
-        self.progress_started.connect(lambda: print("Scan progress started"))
 
     def connect_to_queue(self):
         """
diff --git a/tests/end-2-end/test_rpc_widgets_e2e.py b/tests/end-2-end/test_rpc_widgets_e2e.py
index 19e8109fc..5652701b7 100644
--- a/tests/end-2-end/test_rpc_widgets_e2e.py
+++ b/tests/end-2-end/test_rpc_widgets_e2e.py
@@ -69,7 +69,7 @@ def create_widget(
     return widget
 
 
-@pytest.mark.timeout(100)
+@pytest.mark.timeout(20)
 def test_available_widgets(qtbot, connected_client_gui_obj):
     """This test checks that all widgets that are available via gui.available_widgets can be created and removed."""
     gui = connected_client_gui_obj
diff --git a/tests/unit_tests/test_bec_dispatcher.py b/tests/unit_tests/test_bec_dispatcher.py
index 12b57c673..900fc3c26 100644
--- a/tests/unit_tests/test_bec_dispatcher.py
+++ b/tests/unit_tests/test_bec_dispatcher.py
@@ -1,6 +1,7 @@
 # pylint: disable = no-name-in-module,missing-class-docstring, missing-module-docstring
 import threading
 import time
+from types import SimpleNamespace
 from unittest import mock
 
 import pytest
@@ -213,3 +214,51 @@ def _get_slots():
 
     send_msg_event.set()
     qtbot.wait(10)
+
+
+def test_qt_redis_connector_logs_rpc_before_qt_callback(monkeypatch):
+    info_mock = mock.MagicMock()
+    warning_mock = mock.MagicMock()
+    monkeypatch.setattr("bec_widgets.utils.bec_dispatcher.logger.info", info_mock)
+    monkeypatch.setattr("bec_widgets.utils.bec_dispatcher.logger.warning", warning_mock)
+
+    def callback(_msg, _metadata):
+        pass
+
+    cb = QtThreadSafeCallback(callback)
+    connector = QtRedisConnector("localhost:1", mock.MagicMock())
+    rpc_msg = SimpleNamespace(
+        content={
+            "action": "set_value",
+            "parameter": {"args": [1], "kwargs": {"source": "test"}, "gui_id": "ring"},
+        },
+        metadata={
+            "request_id": "dispatcher-request",
+            "receiver": "gui",
+            "object_name": "progressbar",
+            "timeout": 0.1,
+            "sent_at": 1.0,
+            "deadline": 1.1,
+        },
+    )
+
+    try:
+        connector._execute_callback(cb, {"data": rpc_msg}, {})
+
+        info_mock.assert_called_once()
+        info_message = info_mock.call_args.args[0]
+        assert "GUI RPC dispatcher received request before Qt callback emit" in info_message
+        assert "request_id=dispatcher-request" in info_message
+        assert "method=set_value" in info_message
+        assert "receiver=gui" in info_message
+        assert "target_gui_id=ring" in info_message
+        assert "object_name=progressbar" in info_message
+        assert "timeout=0.1" in info_message
+        assert "stale_on_dispatch=True" in info_message
+
+        warning_mock.assert_called_once()
+        warning_message = warning_mock.call_args.args[0]
+        assert "received request after client timeout deadline" in warning_message
+        assert "request_id=dispatcher-request" in warning_message
+    finally:
+        connector.shutdown()
diff --git a/tests/unit_tests/test_client_utils.py b/tests/unit_tests/test_client_utils.py
index 30f0a5daa..5cf5750f6 100644
--- a/tests/unit_tests/test_client_utils.py
+++ b/tests/unit_tests/test_client_utils.py
@@ -1,10 +1,18 @@
+import signal
+import subprocess
 from contextlib import contextmanager
 from unittest import mock
 
 import pytest
 
 from bec_widgets.cli.client import BECDockArea
-from bec_widgets.cli.client_utils import BECGuiClient, _start_plot_process
+from bec_widgets.cli.client_utils import (
+    GRACEFUL_SERVER_SHUTDOWN_RPC_TIMEOUT,
+    OUTPUT_READER_STOP_EVENT_ATTR,
+    BECGuiClient,
+    _join_process_output_thread,
+    _start_plot_process,
+)
 from bec_widgets.cli.rpc.rpc_base import RPCBase, RPCResponseTimeoutError, rpc_timeout
 
 
@@ -262,7 +270,105 @@ def test_client_utils_delete_falls_back_to_direct_close():
 
 def test_client_utils_gui_client_set_rpc_timeout():
     gui = BECGuiClient()
-    assert gui._rpc_timeout == 5
+    assert gui._rpc_timeout == 60
 
     gui.set_rpc_timeout(10)
     assert gui._rpc_timeout == 10
+
+
+def test_client_utils_kill_server_waits_for_process_before_joining_output_thread():
+    gui = BECGuiClient()
+    gui._client = mock.MagicMock()
+    gui._process = mock.MagicMock(pid=123, stdout=None, stderr=None)
+    gui._process.poll.return_value = None
+    order = []
+    gui._process.wait.side_effect = lambda timeout: order.append("wait")
+    gui._process_output_processing_thread = mock.MagicMock()
+    gui._process_output_processing_thread.join.side_effect = lambda timeout: order.append("join")
+    gui._process_output_processing_thread.is_alive.return_value = False
+
+    with (
+        mock.patch.object(gui, "_request_server_shutdown", return_value=False),
+        mock.patch("bec_widgets.cli.client_utils.os.getpgid", return_value=123),
+        mock.patch("bec_widgets.cli.client_utils.os.killpg") as killpg,
+    ):
+        gui.kill_server()
+
+    killpg.assert_called_once_with(123, signal.SIGTERM)
+    assert order == ["wait", "join"]
+    assert gui._process is None
+    assert gui._process_output_processing_thread is None
+
+
+def test_client_utils_kill_server_requests_graceful_shutdown_before_signal():
+    gui = BECGuiClient()
+    gui._client = mock.MagicMock()
+    process = mock.MagicMock(stdout=None, stderr=None)
+    process.poll.return_value = None
+    gui._process = process
+    gui._process_output_processing_thread = mock.MagicMock()
+    gui._process_output_processing_thread.is_alive.return_value = False
+    launcher = mock.MagicMock()
+
+    with (
+        mock.patch.object(
+            BECGuiClient, "launcher", new_callable=mock.PropertyMock
+        ) as launcher_prop,
+        mock.patch("bec_widgets.cli.client_utils.os.killpg") as killpg,
+    ):
+        launcher_prop.return_value = launcher
+        gui.kill_server()
+
+    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
+    assert gui._process_output_processing_thread is None
+
+
+def test_client_utils_kill_server_kills_process_group_after_timeout():
+    gui = BECGuiClient()
+    gui._client = mock.MagicMock()
+    process = mock.MagicMock(pid=123, stdout=None, stderr=None, args=["bec-gui-server"])
+    process.poll.return_value = None
+    process.wait.side_effect = [subprocess.TimeoutExpired(cmd="bec-gui-server", timeout=10), None]
+    gui._process = process
+
+    with (
+        mock.patch.object(gui, "_request_server_shutdown", return_value=False),
+        mock.patch("bec_widgets.cli.client_utils.os.getpgid", return_value=123),
+        mock.patch("bec_widgets.cli.client_utils.os.killpg") as killpg,
+        mock.patch("bec_widgets.cli.client_utils.subprocess.run") as run,
+    ):
+        run.return_value.stdout = "PID PPID PGID STAT COMMAND\n123 1 123 S bec-gui-server"
+        gui.kill_server()
+
+    assert killpg.call_args_list == [mock.call(123, signal.SIGTERM), mock.call(123, signal.SIGKILL)]
+    assert process.wait.call_args_list == [mock.call(timeout=10), mock.call(timeout=10)]
+    run.assert_called_once_with(
+        ["ps", "-o", "pid,ppid,pgid,stat,command", "-g", "123"],
+        check=False,
+        capture_output=True,
+        text=True,
+        timeout=2,
+    )
+
+
+def test_join_process_output_thread_signals_reader_before_closing_streams():
+    process = mock.MagicMock(pid=123, args=["bec-gui-server"])
+    process.stdout = mock.MagicMock()
+    process.stderr = mock.MagicMock()
+    thread = mock.MagicMock()
+    stop_event = mock.MagicMock()
+    setattr(thread, OUTPUT_READER_STOP_EVENT_ATTR, stop_event)
+    thread.is_alive.side_effect = [True, False]
+    logger = mock.MagicMock()
+
+    _join_process_output_thread(process, thread, logger)
+
+    assert thread.join.call_args_list == [mock.call(timeout=2), mock.call(timeout=2)]
+    stop_event.set.assert_called_once_with()
+    process.stdout.close.assert_called_once_with()
+    process.stderr.close.assert_called_once_with()
diff --git a/tests/unit_tests/test_launch_window.py b/tests/unit_tests/test_launch_window.py
index 44df9022f..90b942f44 100644
--- a/tests/unit_tests/test_launch_window.py
+++ b/tests/unit_tests/test_launch_window.py
@@ -153,6 +153,17 @@ def test_gui_server_turns_off_the_lights(bec_launch_window, connection_names, hi
             mock_set_quit_on_last_window_closed.assert_called_once_with(True)
 
 
+def test_launcher_detects_external_main_window_without_info_log(bec_launch_window):
+    connection = mock.MagicMock()
+    connection.parent.return_value = None
+    connection.objectName.return_value = "BECMainWindowNoRPC"
+
+    with mock.patch("bec_widgets.applications.launch_window.logger.info") as mock_info:
+        assert not bec_launch_window._launcher_is_last_widget({"window": connection})
+
+    mock_info.assert_not_called()
+
+
 @pytest.mark.parametrize(
     "connection_names, close_called",
     [
diff --git a/tests/unit_tests/test_rpc_base.py b/tests/unit_tests/test_rpc_base.py
index 3fddb4e77..ac6686542 100644
--- a/tests/unit_tests/test_rpc_base.py
+++ b/tests/unit_tests/test_rpc_base.py
@@ -3,10 +3,12 @@
 import pytest
 from bec_lib.device import DeviceBaseWithConfig, Signal
 
+from bec_widgets.cli.rpc import rpc_base as rpc_base_module
 from bec_widgets.cli.rpc.rpc_base import (
     DeletedWidgetError,
     RPCBase,
     RPCReference,
+    RPCResponseTimeoutError,
     _transform_args_kwargs,
 )
 
@@ -51,3 +53,33 @@ def test_transform_args_kwargs():
     )
     assert args == ("full name", "short name", "string_arg", "full name")
     assert kwargs == {"a": "full name", "b": "short name", "c": "string_arg", "d": "full name"}
+
+
+def test_run_rpc_logs_response_timeout(monkeypatch):
+    rpc = RPCBase(gui_id="progress_widget", object_name="progressbar")
+    rpc._rpc_timeout = 0
+    rpc._client = MagicMock()
+
+    info_mock = MagicMock()
+    error_mock = MagicMock()
+    monkeypatch.setattr(rpc_base_module.logger, "info", info_mock)
+    monkeypatch.setattr(rpc_base_module.logger, "error", error_mock)
+
+    with pytest.raises(RPCResponseTimeoutError):
+        rpc._run_rpc("set_value", 42, precision=2, timeout=0)
+
+    publish_msg = rpc._client.connector.set_and_publish.call_args.args[1]
+    assert publish_msg.metadata["method"] == "set_value"
+    assert publish_msg.metadata["target_gui_id"] == "progress_widget"
+    assert publish_msg.metadata["object_name"] == "progressbar"
+    assert publish_msg.metadata["timeout"] == 0
+    assert publish_msg.metadata["deadline"] == publish_msg.metadata["sent_at"]
+    assert info_mock.call_count == 1
+    info_message = info_mock.call_args.args[0]
+    error_mock.assert_called_once()
+    error_message = error_mock.call_args.args[0]
+    assert "GUI RPC response timeout" in error_message
+    assert "method=set_value" in error_message
+    assert "target_gui_id=progress_widget" in error_message
+    assert "object_name=progressbar" in error_message
+    assert "timeout=0" in error_message
diff --git a/tests/unit_tests/test_rpc_server.py b/tests/unit_tests/test_rpc_server.py
index 7f83ea13f..fa8ebf14d 100644
--- a/tests/unit_tests/test_rpc_server.py
+++ b/tests/unit_tests/test_rpc_server.py
@@ -1,11 +1,13 @@
 import argparse
-from unittest.mock import patch
+from unittest.mock import MagicMock, patch
 
 import pytest
 from bec_lib.service_config import ServiceConfig
 from qtpy.QtWidgets import QWidget
 
+from bec_widgets.applications import companion_app as companion_app_module
 from bec_widgets.applications.companion_app import GUIServer
+from bec_widgets.utils import rpc_server as rpc_server_module
 from bec_widgets.utils.bec_connector import BECConnector
 from bec_widgets.utils.rpc_server import RegistryNotReadyError, RPCServer, SingleshotRPCRepeat
 
@@ -58,6 +60,68 @@ def test_gui_server_get_service_config(gui_server):
     assert gui_server._get_service_config().config == ServiceConfig().config
 
 
+def test_gui_server_signal_shutdown_closes_widgets_and_quits_app(gui_server):
+    widget = MagicMock()
+    gui_server.app = MagicMock()
+    gui_server.app.topLevelWidgets.return_value = [widget]
+
+    gui_server.request_shutdown()
+
+    widget.close.assert_called_once()
+    gui_server.app.quit.assert_called_once()
+
+
+def test_gui_server_shutdown_is_idempotent(gui_server):
+    gui_server.launcher_window = MagicMock()
+    gui_server.dispatcher = MagicMock()
+
+    with (
+        patch.object(companion_app_module.shiboken6, "isValid", return_value=True),
+        patch.object(companion_app_module.pylsp_server, "is_running", return_value=False),
+    ):
+        gui_server.shutdown()
+        gui_server.shutdown()
+
+    gui_server.launcher_window.close.assert_called_once()
+    gui_server.launcher_window.deleteLater.assert_called_once()
+    gui_server.dispatcher.stop_cli_server.assert_called_once()
+    gui_server.dispatcher.disconnect_all.assert_called_once()
+
+
+def test_rpc_server_system_capabilities_include_shutdown(rpc_server):
+    assert rpc_server.run_system_rpc("system.list_capabilities", [], {}) == {
+        "system.launch_dock_area": True,
+        "system.shutdown": True,
+    }
+
+
+def test_rpc_server_system_shutdown_requests_gui_server_shutdown(rpc_server, qapp):
+    gui_server = MagicMock()
+    qapp.gui_server = gui_server
+
+    rpc_server.run_system_rpc("system.shutdown", [], {})
+    qapp.processEvents()
+
+    gui_server.request_shutdown.assert_called_once()
+    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.
@@ -91,22 +155,34 @@ def serialize_side_effect(obj):
         # Third call succeeds
         return {"gui_id": dummy.gui_id, "success": True}
 
+    warning_mock = MagicMock()
+
     # Patch serialize_object to control when it raises RegistryNotReadyError
     with patch.object(rpc_server, "serialize_object", side_effect=serialize_side_effect):
         with patch.object(rpc_server, "send_response") as mock_send_response:
-            # Start the serialization process
-            rpc_server._rpc_singleshot_repeats[request_id] = SingleshotRPCRepeat()
-            rpc_server.serialize_result_and_send(request_id, dummy)
-
-            # Verify that serialize_object was called 3 times
-            qtbot.waitUntil(lambda: call_count >= 3, timeout=5000)
-
-            # Verify that send_response was called with success
-            mock_send_response.assert_called_once()
-            args = mock_send_response.call_args[0]
-            assert args[0] == request_id
-            assert args[1] is True  # accepted=True
-            assert "result" in args[2]
+            with patch.object(rpc_server_module.logger, "warning", warning_mock):
+                # Start the serialization process
+                rpc_server._rpc_singleshot_repeats[request_id] = SingleshotRPCRepeat()
+                rpc_server.serialize_result_and_send(request_id, dummy)
+
+                # Verify that serialize_object was called 3 times
+                qtbot.waitUntil(lambda: call_count >= 3, timeout=5000)
+
+                # Verify that send_response was called with success
+                mock_send_response.assert_called_once()
+                args = mock_send_response.call_args[0]
+                assert args[0] == request_id
+                assert args[1] is True  # accepted=True
+                assert "result" in args[2]
+
+    assert warning_mock.call_count == 2
+    warning_logs = "\n".join(call.args[0] for call in warning_mock.call_args_list)
+    assert "result serialization delayed; retrying" in warning_logs
+    assert "request_id=test_request_123" in warning_logs
+    assert "retry_delay_ms=100" in warning_logs
+    assert "accumulated_delay_ms=100" in warning_logs
+    assert "accumulated_delay_ms=200" in warning_logs
+    assert "max_delay_ms=2000" in warning_logs
 
 
 def test_serialize_result_and_send_max_delay_exceeded(rpc_server, qtbot, dummy_widget):
@@ -140,6 +216,56 @@ def test_serialize_result_and_send_max_delay_exceeded(rpc_server, qtbot, dummy_w
             assert "Max delay exceeded" in args[2]["error"]
 
 
+def test_send_response_logs_publish_status(rpc_server, monkeypatch):
+    info_mock = MagicMock()
+    error_mock = MagicMock()
+    monkeypatch.setattr(rpc_server_module.logger, "info", info_mock)
+    monkeypatch.setattr(rpc_server_module.logger, "error", error_mock)
+
+    with patch.object(rpc_server.client.connector, "set_and_publish") as publish_mock:
+        rpc_server.send_response("request-ok", True, {"result": None})
+        rpc_server.send_response("request-failed", False, {"error": "bad"})
+
+    assert publish_mock.call_count == 2
+    assert "request_id=request-ok" in info_mock.call_args.args[0]
+    assert "accepted=True" in info_mock.call_args.args[0]
+    assert "request_id=request-failed" in error_mock.call_args.args[0]
+    assert "accepted=False" in error_mock.call_args.args[0]
+
+
+def test_on_rpc_update_logs_late_client_deadline(rpc_server, monkeypatch):
+    info_mock = MagicMock()
+    warning_mock = MagicMock()
+    monkeypatch.setattr(rpc_server_module.logger, "info", info_mock)
+    monkeypatch.setattr(rpc_server_module.logger, "warning", warning_mock)
+
+    rpc_server.rpc_register.get_rpc_by_id = MagicMock()
+    rpc_server.run_rpc = MagicMock(return_value=None)
+    rpc_server.serialize_result_and_send = MagicMock()
+
+    rpc_server.on_rpc_update(
+        {
+            "action": "set_value",
+            "parameter": {"args": [1], "kwargs": {"source": "test"}, "gui_id": "ring"},
+        },
+        {"request_id": "late-request", "timeout": 0.1, "sent_at": 1.0, "deadline": 1.1},
+    )
+
+    received_log = info_mock.call_args_list[0].args[0]
+    executed_log = info_mock.call_args_list[1].args[0]
+    warning_logs = "\n".join(call.args[0] for call in warning_mock.call_args_list)
+
+    assert "GUI RPC server received request" in received_log
+    assert "request_id=late-request" in received_log
+    assert "method=set_value" in received_log
+    assert "target_gui_id=ring" in received_log
+    assert "timeout=0.1" in received_log
+    assert "stale_on_receive=True" in received_log
+    assert "response_after_client_deadline=True" in executed_log
+    assert "received request after client timeout deadline" in warning_logs
+    assert "response is late for client timeout" in warning_logs
+
+
 def test_run_rpc_delegates_to_rpc_content_class(rpc_server):
     class Content:
         USER_ACCESS = ["foo", "mode", "mode.setter"]