diff --git a/spyder/api/widgets/menus.py b/spyder/api/widgets/menus.py
index 219e4faf5f2..0cc59dc52f0 100644
--- a/spyder/api/widgets/menus.py
+++ b/spyder/api/widgets/menus.py
@@ -108,7 +108,11 @@ def add_action(self, action, section=None, before=None,
         self._ordered_actions = []
 
     def remove_action(self, item):
-        self._actions.remove(item)
+        try:
+            self._actions.remove(item)
+        except ValueError:
+            # Skip if the item is not in the menu
+            pass
 
     def get_title(self):
         """
diff --git a/spyder/plugins/application/plugin.py b/spyder/plugins/application/plugin.py
index 3b36f027633..b194e2e4c5b 100644
--- a/spyder/plugins/application/plugin.py
+++ b/spyder/plugins/application/plugin.py
@@ -130,8 +130,20 @@ def on_console_teardown(self):
     @on_plugin_teardown(plugin=Plugins.Shortcuts)
     def on_shortcuts_teardown(self):
         self.shortcuts_available = False
-        if self.main_menu_available:
-            self._depopulate_help_menu()
+
+    @on_plugin_teardown(plugin=Plugins.MainMenu)
+    def on_main_menu_teardown(self):
+        main_menu = self.get_plugin(Plugins.MainMenu)
+        self.main_menu_available = False
+
+        self._depopulate_file_menu()
+        self._depopulate_tools_menu()
+        self._depopulate_help_menu()
+
+        report_action = self.get_action(ConsoleActions.SpyderReportAction)
+        main_menu.remove_item_from_application_menu(
+            report_action,
+            menu_id=ApplicationMenus.Help)
 
     def on_close(self, _unused=True):
         self.get_container().on_close()
@@ -176,12 +188,6 @@ def _populate_help_menu(self):
         self._populate_help_menu_support_section(mainmenu)
         self._populate_help_menu_about_section(mainmenu)
 
-    def _depopulate_help_menu(self):
-        mainmenu = self.get_plugin(Plugins.MainMenu)
-        self._depopulate_help_menu_documentation_section(mainmenu)
-        self._depopulate_help_menu_support_section(mainmenu)
-        self._populate_help_menu_about_section(mainmenu)
-
     def _populate_help_menu_documentation_section(self, mainmenu):
         """Add base Spyder documentation actions to the Help main menu."""
         if mainmenu:
@@ -220,6 +226,28 @@ def _populate_help_menu_about_section(self, mainmenu):
                 menu_id=ApplicationMenus.Help,
                 section=HelpMenuSections.About)
 
+    def _depopulate_file_menu(self):
+        mainmenu = self.get_plugin(Plugins.MainMenu)
+        if mainmenu:
+            mainmenu.remove_item_from_application_menu(
+                self.restart_action,
+                menu_id=ApplicationMenus.File)
+
+    def _depopulate_tools_menu(self):
+        """Add base actions and menus to the Tools menu."""
+        mainmenu = self.get_plugin(Plugins.MainMenu)
+        if mainmenu:
+            if WinUserEnvDialog is not None:
+                mainmenu.remove_item_from_application_menu(
+                    self.winenv_action,
+                    menu_id=ApplicationMenus.Tools)
+
+    def _depopulate_help_menu(self):
+        mainmenu = self.get_plugin(Plugins.MainMenu)
+        self._depopulate_help_menu_documentation_section(mainmenu)
+        self._depopulate_help_menu_support_section(mainmenu)
+        self._depopulate_help_menu_about_section(mainmenu)
+
     def _depopulate_help_menu_documentation_section(self, mainmenu):
         if mainmenu:
             for documentation_action in [