diff --git a/src/controller/python/chip/ChipReplStartup.py b/src/controller/python/chip/ChipReplStartup.py
index 861d07ca8a7c9b..efdf8ea4cb3b6b 100644
--- a/src/controller/python/chip/ChipReplStartup.py
+++ b/src/controller/python/chip/ChipReplStartup.py
@@ -12,6 +12,7 @@
 import argparse
 import builtins
 import chip.FabricAdmin
+import atexit
 
 _fabricAdmins = None
 
@@ -98,6 +99,12 @@ def ReplInit(debug):
         logging.getLogger().setLevel(logging.WARN)
 
 
+def StackShutdown():
+    chip.FabricAdmin.FabricAdmin.ShutdownAll()
+    ChipDeviceCtrl.ChipDeviceController.ShutdownAll()
+    builtins.chipStack.Shutdown()
+
+
 def matterhelp(classOrObj=None):
     if (classOrObj is None):
         inspect(builtins.devCtrl, methods=True, help=True, private=False)
@@ -135,5 +142,7 @@ def mattersetdebug(enableDebugMode: bool = True):
 
 builtins.devCtrl = devCtrl
 
+atexit.register(StackShutdown)
+
 console.print(
     '\n\n[blue]Default CHIP Device Controller has been initialized to manage [bold red]fabricAdmins[0][blue], and is available as [bold red]devCtrl')
diff --git a/src/controller/python/chip/ChipStack.py b/src/controller/python/chip/ChipStack.py
index 47c5ef43ce14c8..666d1192f7a9f8 100644
--- a/src/controller/python/chip/ChipStack.py
+++ b/src/controller/python/chip/ChipStack.py
@@ -318,6 +318,9 @@ def setLogFunct(self, logFunct):
             self._ChipStackLib.pychip_Stack_SetLogFunct(logFunct)
 
     def Shutdown(self):
+        # Make sure PersistentStorage is destructed before chipStack
+        # to avoid accessing builtins.chipStack after destruction.
+        self._persistentStorage = None
         self.Call(lambda: self._ChipStackLib.pychip_Stack_Shutdown())
         self.networkLock = None
         self.completeEvent = None