diff --git a/bec_widgets/applications/companion_app.py b/bec_widgets/applications/companion_app.py
index f229b677..43524194 100644
--- a/bec_widgets/applications/companion_app.py
+++ b/bec_widgets/applications/companion_app.py
@@ -5,6 +5,7 @@ import json
 import os
 import signal
 import sys
+import traceback
 from contextlib import redirect_stderr, redirect_stdout
 
 import darkdetect
@@ -63,6 +64,7 @@ class GUIServer:
         self.app: QApplication | None = None
         self.launcher_window: LaunchWindow | None = None
         self.dispatcher: BECDispatcher | None = None
+        self._shutdown_started = False
 
     def start(self):
         """
@@ -123,17 +125,8 @@ class GUIServer:
         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())
 
@@ -150,16 +143,67 @@ class GUIServer:
         )
         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/cli/client_utils.py b/bec_widgets/cli/client_utils.py
index 551e41b8..57443805 100644
--- a/bec_widgets/cli/client_utils.py
+++ b/bec_widgets/cli/client_utils.py
@@ -5,6 +5,7 @@ from __future__ import annotations
 import json
 import os
 import select
+import signal
 import subprocess
 import threading
 import time
@@ -33,6 +34,9 @@ else:
 logger = bec_logger.logger
 
 IGNORE_WIDGETS = ["LaunchWindow"]
+PROCESS_TERMINATION_TIMEOUT = 10
+PROCESS_OUTPUT_THREAD_JOIN_TIMEOUT = 2
+GRACEFUL_SERVER_SHUTDOWN_TIMEOUT = 5
 
 RegistryState: TypeAlias = dict[
     Literal["gui_id", "name", "widget_class", "config", "__rpc__", "container_proxy"],
@@ -75,6 +79,123 @@ 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(
+            f"Failed to terminate GUI process group: {exc}; terminating process only. "
+            f"{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)}"
+        )
+
+    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
+
+    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)}")
+            pass
+    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)}"
+        )
+
+
 def _start_plot_process(
     gui_id: str,
     gui_class_id: str,
@@ -465,11 +586,13 @@ class BECGuiClient(RPCBase):
 
         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 +611,30 @@ class BECGuiClient(RPCBase):
     #### 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=False
+            )
+        except Exception as exc:
+            logger.warning(
+                f"Could not request graceful GUI shutdown via RPC: {exc}. " f"{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"
+            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/utils/rpc_server.py b/bec_widgets/utils/rpc_server.py
index af27e4ca..d3b9cf4b 100644
--- a/bec_widgets/utils/rpc_server.py
+++ b/bec_widgets/utils/rpc_server.py
@@ -12,7 +12,7 @@ from bec_lib.endpoints import MessageEndpoints
 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
@@ -290,10 +290,23 @@ class RPCServer:
     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,
@@ -468,8 +481,9 @@ class RPCServer:
                 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/tests/unit_tests/test_client_utils.py b/tests/unit_tests/test_client_utils.py
index 3c489b8a..efce65bd 100644
--- a/tests/unit_tests/test_client_utils.py
+++ b/tests/unit_tests/test_client_utils.py
@@ -1,3 +1,5 @@
+import signal
+import subprocess
 from contextlib import contextmanager
 from unittest import mock
 
@@ -266,3 +268,81 @@ def test_client_utils_gui_client_set_rpc_timeout():
 
     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=False)
+    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,
+    )
diff --git a/tests/unit_tests/test_rpc_server.py b/tests/unit_tests/test_rpc_server.py
index 6ef01531..8b71d8f7 100644
--- a/tests/unit_tests/test_rpc_server.py
+++ b/tests/unit_tests/test_rpc_server.py
@@ -5,6 +5,7 @@ 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
@@ -59,6 +60,52 @@ 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_singleshot_rpc_repeat_raises_on_repeated_singleshot(rpc_server):
     """
     Test that a singleshot RPC method raises an error when called multiple times.