diff --git a/spyder/api/plugins/old_api.py b/spyder/api/plugins/old_api.py
index 22ea49578ae..d86c3df1a6d 100644
--- a/spyder/api/plugins/old_api.py
+++ b/spyder/api/plugins/old_api.py
@@ -321,11 +321,43 @@ def register_shortcut(self, qaction_or_qshortcut, context, name,
             This is useful if the action is added to a toolbar and
             users hover it to see what it does.
         """
-        super(BasePluginWidget, self)._register_shortcut(
+        self.main.register_shortcut(
             qaction_or_qshortcut,
             context,
             name,
-            add_shortcut_to_tip)
+            add_shortcut_to_tip,
+            self.CONF_SECTION)
+
+    def unregister_shortcut(self, qaction_or_qshortcut, context, name,
+                            add_shortcut_to_tip=False):
+        """
+        Unregister a shortcut associated to a QAction or a QShortcut to
+        Spyder main application.
+
+        Parameters
+        ----------
+        qaction_or_qshortcut: QAction or QShortcut
+            QAction to register the shortcut for or QShortcut.
+        context: str
+            Name of the plugin this shortcut applies to. For instance,
+            if you pass 'Editor' as context, the shortcut will only
+            work when the editor is focused.
+            Note: You can use '_' if you want the shortcut to be work
+            for the entire application.
+        name: str
+            Name of the action the shortcut refers to (e.g. 'Debug
+            exit').
+        add_shortcut_to_tip: bool
+            If True, the shortcut is added to the action's tooltip.
+            This is useful if the action is added to a toolbar and
+            users hover it to see what it does.
+        """
+        self.main.unregister_shortcut(
+            qaction_or_qshortcut,
+            context,
+            name,
+            add_shortcut_to_tip,
+            self.CONF_SECTION)
 
     def register_widget_shortcuts(self, widget):
         """
@@ -346,6 +378,24 @@ def register_widget_shortcuts(self, widget):
         for qshortcut, context, name in widget.get_shortcut_data():
             self.register_shortcut(qshortcut, context, name)
 
+    def unregister_widget_shortcuts(self, widget):
+        """
+        Unregister shortcuts defined by a plugin's widget.
+
+        Parameters
+        ----------
+        widget: QWidget
+            Widget to register shortcuts for.
+
+        Notes
+        -----
+        The widget interface must have a method called
+        `get_shortcut_data` for this to work. Please see
+        `spyder/widgets/findreplace.py` for an example.
+        """
+        for qshortcut, context, name in widget.get_shortcut_data():
+            self.unregister_shortcut(qshortcut, context, name)
+
     def get_color_scheme(self):
         """
         Get the current color scheme.
diff --git a/spyder/app/mainwindow.py b/spyder/app/mainwindow.py
index bda93a8c2ed..0a0ddc6dace 100644
--- a/spyder/app/mainwindow.py
+++ b/spyder/app/mainwindow.py
@@ -1270,6 +1270,18 @@ def register_shortcut(self, qaction_or_qshortcut, context, name,
                 plugin_name=plugin_name,
             )
 
+    def unregister_shortcut(self, qaction_or_qshortcut, context, name,
+                            add_shortcut_to_tip=True, plugin_name=None):
+        shortcuts = self.get_plugin(Plugins.Shortcuts, error=False)
+        if shortcuts:
+            shortcuts.unregister_shortcut(
+                qaction_or_qshortcut,
+                context,
+                name,
+                add_shortcut_to_tip=add_shortcut_to_tip,
+                plugin_name=plugin_name,
+            )
+
     # --- Other
     def update_source_menu(self):
         """Update source menu options that vary dynamically."""
diff --git a/spyder/app/tests/test_mainwindow.py b/spyder/app/tests/test_mainwindow.py
index 97772240411..09a5c4351d6 100644
--- a/spyder/app/tests/test_mainwindow.py
+++ b/spyder/app/tests/test_mainwindow.py
@@ -11,6 +11,7 @@
 """
 
 # Standard library imports
+import gc
 import os
 import os.path as osp
 import psutil
@@ -350,6 +351,9 @@ def main_window(request, tmpdir, qtbot):
 
                     # Close editor related elements
                     window.editor.close_all_files()
+                    # force close all files
+                    while window.editor.editorstacks[0].close_file(force=True):
+                        pass
                     for editorwindow in window.editor.editorwindows:
                         editorwindow.close()
                     editorstack = window.editor.get_current_editorstack()
@@ -530,6 +534,74 @@ def test_single_instance_and_edit_magic(main_window, qtbot, tmpdir):
     main_window.editor.close_file()
 
 
+@pytest.mark.slow
+@pytest.mark.use_introspection
+def test_leaks(main_window, qtbot):
+    """
+    Test leaks in mainwindow when closing a file or a console.
+
+    Many other ways of leaking exist but are not covered here.
+    """
+    # Wait until the window is fully up
+    shell = main_window.ipyconsole.get_current_shellwidget()
+    qtbot.waitUntil(
+        lambda: shell._prompt_html is not None, timeout=SHELL_TIMEOUT)
+
+    # Count initial objects
+    # Only one of each should be present, but because of many leaks,
+    # this is most likely not the case. Here only closing is tested
+    shell.wait_all_shutdown()
+    gc.collect()
+    objects = gc.get_objects()
+    n_code_editor_init = 0
+    for o in objects:
+        if type(o).__name__ == "CodeEditor":
+            n_code_editor_init += 1
+    n_shell_init = 0
+    for o in objects:
+        if type(o).__name__ == "ShellWidget":
+            n_shell_init += 1
+    del objects
+
+    # Open a second file and console
+    main_window.editor.new()
+    main_window.ipyconsole.create_new_client()
+    # Do something interesting in the new window
+    code_editor = main_window.editor.get_focus_widget()
+    # Show an error in the editor
+    code_editor.set_text("aaa")
+    del code_editor
+
+    shell = main_window.ipyconsole.get_current_shellwidget()
+    qtbot.waitUntil(
+        lambda: shell._prompt_html is not None, timeout=SHELL_TIMEOUT)
+    with qtbot.waitSignal(shell.executed):
+        shell.execute("%debug print()")
+
+    # Close all files and consoles
+    main_window.editor.close_all_files()
+    main_window.ipyconsole.restart()
+
+    # Wait until the shells are closed
+    shell = main_window.ipyconsole.get_current_shellwidget()
+    shell.wait_all_shutdown()
+    # Count final objects
+    gc.collect()
+    objects = gc.get_objects()
+    n_code_editor = 0
+    for o in objects:
+        if type(o).__name__ == "CodeEditor":
+            n_code_editor += 1
+    n_shell = 0
+    for o in objects:
+        if type(o).__name__ == "ShellWidget":
+            n_shell += 1
+
+    # Make sure no new objects have been created
+    assert n_shell <= n_shell_init
+    assert n_code_editor <= n_code_editor_init
+
+
 @pytest.mark.slow
 def test_lock_action(main_window, qtbot):
     """Test the lock interface action."""
diff --git a/spyder/config/main.py b/spyder/config/main.py
index 0d7654fb991..2155163f02b 100644
--- a/spyder/config/main.py
+++ b/spyder/config/main.py
@@ -330,7 +330,6 @@
             ('completions',
              {
                'enable': True,
-               'kite_call_to_action': False,
                'enable_code_snippets': True,
                'completions_wait_for_ms': 200,
                'enabled_providers': {},
@@ -640,4 +639,4 @@
 #    or if you want to *rename* options, then you need to do a MAJOR update in
 #    version, e.g. from 3.0.0 to 4.0.0
 # 3. You don't need to touch this value if you're just adding a new option
-CONF_VERSION = '70.4.0'
+CONF_VERSION = '71.0.0'
diff --git a/spyder/plugins/base.py b/spyder/plugins/base.py
index 158d0076580..976793e9291 100644
--- a/spyder/plugins/base.py
+++ b/spyder/plugins/base.py
@@ -465,16 +465,6 @@ def _setup(self):
         self.sig_update_plugin_title.connect(self._update_plugin_title)
         self.setWindowTitle(self.get_plugin_title())
 
-    def _register_shortcut(self, qaction_or_qshortcut, context, name,
-                           add_shortcut_to_tip=False):
-        """Register a shortcut associated to a QAction or QShortcut."""
-        self.main.register_shortcut(
-            qaction_or_qshortcut,
-            context,
-            name,
-            add_shortcut_to_tip,
-            self.CONF_SECTION)
-
     def _get_color_scheme(self):
         """Get the current color scheme."""
         return get_color_scheme(CONF.get('appearance', 'selected'))
diff --git a/spyder/plugins/completion/plugin.py b/spyder/plugins/completion/plugin.py
index 3a9139290b2..e816a65b236 100644
--- a/spyder/plugins/completion/plugin.py
+++ b/spyder/plugins/completion/plugin.py
@@ -18,6 +18,7 @@
 import os
 from pkg_resources import parse_version, iter_entry_points
 from typing import List, Union
+import weakref
 
 # Third-party imports
 from qtpy.QtCore import QMutex, QMutexLocker, QTimer, Slot, Signal
@@ -1020,7 +1021,7 @@ def send_request(self, language: str, req_type: str, req: dict):
         self.requests[req_id] = {
             'language': language,
             'req_type': req_type,
-            'response_instance': req['response_instance'],
+            'response_instance': weakref.ref(req['response_instance']),
             'sources': {},
             'timed_out': False,
         }
@@ -1239,7 +1240,7 @@ def skip_and_reply(self, req_id: int):
         """
         request_responses = self.requests[req_id]
         req_type = request_responses['req_type']
-        response_instance = id(request_responses['response_instance'])
+        response_instance = id(request_responses['response_instance']())
         do_send = True
 
         # This is necessary to prevent sending completions for old requests
@@ -1248,7 +1249,7 @@ def skip_and_reply(self, req_id: int):
             max_req_id = max(
                 [key for key, item in self.requests.items()
                  if item['req_type'] == req_type
-                 and id(item['response_instance']) == response_instance]
+                 and id(item['response_instance']()) == response_instance]
                 or [-1])
             do_send = (req_id == max_req_id)
 
@@ -1266,7 +1267,7 @@ def gather_and_reply(self, request_responses: dict):
         """
         req_type = request_responses['req_type']
         req_id_responses = request_responses['sources']
-        response_instance = request_responses['response_instance']
+        response_instance = request_responses['response_instance']()
         logger.debug('Gather responses for {0}'.format(req_type))
 
         if req_type == CompletionRequestTypes.DOCUMENT_COMPLETION:
@@ -1275,7 +1276,8 @@ def gather_and_reply(self, request_responses: dict):
             responses = self.gather_responses(req_type, req_id_responses)
 
         try:
-            response_instance.handle_response(req_type, responses)
+            if response_instance:
+                response_instance.handle_response(req_type, responses)
         except RuntimeError:
             # This is triggered when a codeeditor instance has been
             # removed before the response can be processed.
diff --git a/spyder/plugins/completion/providers/kite/widgets/__init__.py b/spyder/plugins/completion/providers/kite/widgets/__init__.py
index 0e076f99fd6..7a2ee828b67 100644
--- a/spyder/plugins/completion/providers/kite/widgets/__init__.py
+++ b/spyder/plugins/completion/providers/kite/widgets/__init__.py
@@ -8,4 +8,3 @@
 
 from .messagebox import KiteInstallationErrorMessage
 from .status import KiteStatusWidget
-from .calltoaction import KiteCallToAction
diff --git a/spyder/plugins/completion/providers/kite/widgets/calltoaction.py b/spyder/plugins/completion/providers/kite/widgets/calltoaction.py
deleted file mode 100644
index 100bffa4fed..00000000000
--- a/spyder/plugins/completion/providers/kite/widgets/calltoaction.py
+++ /dev/null
@@ -1,145 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright © Spyder Project Contributors
-# Licensed under the terms of the MIT License
-# (see spyder/__init__.py for details)
-
-from qtpy.QtCore import Qt
-from qtpy.QtWidgets import (QLabel, QVBoxLayout, QFrame,
-                            QHBoxLayout, QPushButton)
-
-from spyder.api.config.mixins import SpyderConfigurationAccessor
-from spyder.config.base import _
-from spyder.plugins.completion.providers.kite.bloomfilter import (
-    KiteBloomFilter)
-from spyder.plugins.completion.providers.kite.parsing import (
-    find_returning_function_path)
-from spyder.plugins.completion.providers.kite.utils.status import (
-    check_if_kite_installed)
-from spyder.plugins.completion.providers.fallback.actor import (
-    FALLBACK_COMPLETION)
-from spyder.utils.palette import QStylePalette
-
-
-COVERAGE_MESSAGE = (
-    _("No completions found."
-      " Get completions for this case and more by installing Kite.")
-)
-
-
-class KiteCallToAction(QFrame, SpyderConfigurationAccessor):
-    CONF_SECTION = 'completions'
-
-    def __init__(self, textedit, ancestor):
-        super(KiteCallToAction, self).__init__(ancestor)
-        self.textedit = textedit
-
-        self.setFrameStyle(QFrame.StyledPanel | QFrame.Plain)
-        self.setAutoFillBackground(True)
-        self.setWindowFlags(Qt.SubWindow | Qt.FramelessWindowHint)
-        self.setFocusPolicy(Qt.NoFocus)
-        self.setObjectName("kite-call-to-action")
-        self.setStyleSheet(self.styleSheet() +
-                           ("#kite-call-to-action "
-                            "{{ border: 1px solid; "
-                            "  border-color: {border_color}; "
-                            "  border-radius: 4px;}} "
-                            "#kite-call-to-action:hover "
-                            "{{ border:1px solid {border}; }}").format(
-                            border_color=QStylePalette.COLOR_BACKGROUND_4,
-                            border=QStylePalette.COLOR_ACCENT_4))
-
-        # sub-layout: horizontally aligned links
-        actions = QFrame(self)
-        actions_layout = QHBoxLayout()
-        actions_layout.setContentsMargins(5, 5, 5, 5)
-        actions_layout.setSpacing(10)
-        actions_layout.addStretch()
-        actions.setLayout(actions_layout)
-
-        self._install_button = QPushButton(_("Install Kite"))
-        self._dismiss_button = QPushButton(_("Dismiss Forever"))
-        self._install_button.clicked.connect(self._install_kite)
-        self._dismiss_button.clicked.connect(self._dismiss_forever)
-        actions_layout.addWidget(self._install_button)
-        actions_layout.addWidget(self._dismiss_button)
-
-        # main layout: message + horizontally aligned links
-        main_layout = QVBoxLayout()
-        main_layout.setContentsMargins(5, 5, 5, 5)
-        self.setLayout(main_layout)
-        self.label = QLabel(self)
-        self.label.setWordWrap(True)
-        main_layout.addWidget(self.label)
-        main_layout.addWidget(actions)
-        main_layout.addStretch()
-
-        self._enabled = self.get_conf('kite_call_to_action')
-        self._escaped = False
-        self.hide()
-
-        is_kite_installed, __ = check_if_kite_installed()
-
-        if is_kite_installed:
-            self._dismiss_forever()
-
-    def handle_key_press(self, event):
-        key = event.key()
-        if not self._is_valid_ident_key(key):
-            self.hide()
-        self._escaped = key == Qt.Key_Escape
-
-    def handle_mouse_press(self, event):
-        self.hide()
-
-    def handle_processed_completions(self, completions):
-        if not self.get_conf('kite_call_to_action'):
-            return
-
-        installers_available = self.get_conf(
-            ('provider_configuration', 'kite', 'values',
-             'installers_available'))
-
-        if not installers_available:
-            return
-
-        if self._escaped:
-            return
-        if not self.textedit.completion_widget.isHidden():
-            return
-        if any(c['provider'] != FALLBACK_COMPLETION for c in completions):
-            return
-
-        # check if we should show the CTA, based on Kite support
-        text = self.textedit.get_text('sof', 'eof')
-        offset = self.textedit.get_position('cursor')
-
-        fn_path = find_returning_function_path(text, offset, u'\u2029')
-        if fn_path is None:
-            return
-        if not KiteBloomFilter.is_valid_path(fn_path):
-            return
-
-        self.label.setText(COVERAGE_MESSAGE)
-        self.resize(self.sizeHint())
-        self.show()
-        self.textedit.position_widget_at_cursor(self)
-        self.raise_()
-
-    def _is_valid_ident_key(self, key):
-        is_upper = ord('A') <= key <= ord('Z')
-        is_lower = ord('a') <= key <= ord('z')
-        is_digit = ord('0') <= key <= ord('9')
-        is_under = key == ord('_')
-        return is_upper or is_lower or is_digit or is_under
-
-    def _dismiss_forever(self):
-        self.hide()
-        self._enabled = False
-        self.set_conf('kite_call_to_action', False)
-
-    def _install_kite(self):
-        self.hide()
-        self._enabled = False
-        kite = self.parent().completions.get_provider('kite')
-        kite.show_kite_installation()
diff --git a/spyder/plugins/completion/providers/languageserver/provider.py b/spyder/plugins/completion/providers/languageserver/provider.py
index 16152ec4d03..e8959e13a2a 100644
--- a/spyder/plugins/completion/providers/languageserver/provider.py
+++ b/spyder/plugins/completion/providers/languageserver/provider.py
@@ -148,6 +148,8 @@ def __del__(self):
             try:
                 if self.clients_hearbeat[language] is not None:
                     self.clients_hearbeat[language].stop()
+                    self.clients_hearbeat[language].setParent(None)
+                    del self.clients_hearbeat[language]
             except (TypeError, KeyError, RuntimeError):
                 pass
 
@@ -184,11 +186,12 @@ def restart_lsp(self, language: str, force=False):
                 self.clients_restart_timers[language] = None
                 try:
                     self.clients_hearbeat[language].stop()
+                    self.clients_hearbeat[language].setParent(None)
+                    del self.clients_hearbeat[language]
                     client['instance'].disconnect()
                     client['instance'].stop()
                 except (TypeError, KeyError, RuntimeError):
                     pass
-                self.clients_hearbeat[language] = None
                 self.report_lsp_down(language)
 
     def create_statusbar(self, parent):
@@ -261,6 +264,8 @@ def handle_lsp_down(self, language):
                 and not running_under_pytest()):
             try:
                 self.clients_hearbeat[language].stop()
+                self.clients_hearbeat[language].setParent(None)
+                del self.clients_hearbeat[language]
             except KeyError:
                 pass
             logger.info("Automatic restart for {}...".format(language))
@@ -464,12 +469,15 @@ def start_completion_services_for_language(self, language):
 
             started = language_client['status'] == self.RUNNING
 
-            # Start client heartbeat
-            timer = QTimer(self)
-            self.clients_hearbeat[language] = timer
-            timer.setInterval(self.TIME_HEARTBEAT)
-            timer.timeout.connect(functools.partial(self.check_heartbeat, language))
-            timer.start()
+            if language not in self.clients_hearbeat:
+                # completion_services for language is already running
+                # Start client heartbeat
+                timer = QTimer(self)
+                self.clients_hearbeat[language] = timer
+                timer.setInterval(self.TIME_HEARTBEAT)
+                timer.timeout.connect(functools.partial(
+                    self.check_heartbeat, language))
+                timer.start()
 
             if language_client['status'] == self.STOPPED:
                 config = language_client['config']
@@ -659,6 +667,8 @@ def stop_completion_services_for_language(self, language):
                 try:
                     if self.clients_hearbeat[language] is not None:
                         self.clients_hearbeat[language].stop()
+                        self.clients_hearbeat[language].setParent(None)
+                        del self.clients_hearbeat[language]
                 except (TypeError, KeyError, RuntimeError):
                     pass
                 language_client['instance'].stop()
diff --git a/spyder/plugins/completion/providers/languageserver/providers/document.py b/spyder/plugins/completion/providers/languageserver/providers/document.py
index 659515d1233..ac2427b7087 100644
--- a/spyder/plugins/completion/providers/languageserver/providers/document.py
+++ b/spyder/plugins/completion/providers/languageserver/providers/document.py
@@ -309,7 +309,7 @@ def document_did_close(self, params):
                 if id(codeeditor) == id(editor):
                     idx = i
                     break
-            if idx > 0:
+            if idx >= 0:
                 editors.pop(idx)
 
             if len(editors) == 0:
diff --git a/spyder/plugins/editor/plugin.py b/spyder/plugins/editor/plugin.py
index 6977f10d0e5..6efe9cef04a 100644
--- a/spyder/plugins/editor/plugin.py
+++ b/spyder/plugins/editor/plugin.py
@@ -1332,9 +1332,7 @@ def update_font(self):
             completion_size = CONF.get('main', 'completion/size')
             for finfo in editorstack.data:
                 comp_widget = finfo.editor.completion_widget
-                kite_call_to_action = finfo.editor.kite_call_to_action
                 comp_widget.setup_appearance(completion_size, font)
-                kite_call_to_action.setFont(font)
 
     def set_ancestor(self, ancestor):
         """
@@ -1348,7 +1346,6 @@ def set_ancestor(self, ancestor):
         for editorstack in self.editorstacks:
             for finfo in editorstack.data:
                 comp_widget = finfo.editor.completion_widget
-                kite_call_to_action = finfo.editor.kite_call_to_action
 
                 # This is necessary to catch an error when the plugin is
                 # undocked and docked back, and (probably) a completion is
@@ -1356,7 +1353,6 @@ def set_ancestor(self, ancestor):
                 # Fixes spyder-ide/spyder#17486
                 try:
                     comp_widget.setParent(ancestor)
-                    kite_call_to_action.setParent(ancestor)
                 except RuntimeError:
                     pass
 
diff --git a/spyder/plugins/editor/utils/decoration.py b/spyder/plugins/editor/utils/decoration.py
index 4417a89f139..a77eb182c24 100644
--- a/spyder/plugins/editor/utils/decoration.py
+++ b/spyder/plugins/editor/utils/decoration.py
@@ -135,11 +135,15 @@ def _update(self):
         NOTE: Update TextDecorations to use editor font, using a different
         font family and point size could cause unwanted behaviors.
         """
+        editor = self.editor
+        if editor is None:
+            return
+
         try:
-            font = self.editor.font()
+            font = editor.font()
 
             # Get the current visible block numbers
-            first, last = self.editor.get_buffer_block_numbers()
+            first, last = editor.get_buffer_block_numbers()
 
             # Update visible decorations
             visible_decorations = []
@@ -166,7 +170,7 @@ def _update(self):
                         decoration.format.setFontFamily(font.family())
                         decoration.format.setFontPointSize(font.pointSize())
 
-            self.editor.setExtraSelections(visible_decorations)
+            editor.setExtraSelections(visible_decorations)
         except RuntimeError:
             # This is needed to fix spyder-ide/spyder#9173.
             return
diff --git a/spyder/plugins/editor/widgets/codeeditor.py b/spyder/plugins/editor/widgets/codeeditor.py
index 7094309a60e..998597e9a3d 100644
--- a/spyder/plugins/editor/widgets/codeeditor.py
+++ b/spyder/plugins/editor/widgets/codeeditor.py
@@ -56,7 +56,6 @@
                                               QMenuOnlyForEnter,
                                               EditorExtensionsManager,
                                               SnippetsExtension)
-from spyder.plugins.completion.providers.kite.widgets import KiteCallToAction
 from spyder.plugins.completion.api import (CompletionRequestTypes,
                                            TextDocumentSyncKind,
                                            DiagnosticSeverity)
@@ -599,7 +598,6 @@ def __init__(self, parent=None):
 
         # re-use parent of completion_widget (usually the main window)
         completion_parent = self.completion_widget.parent()
-        self.kite_call_to_action = KiteCallToAction(self, completion_parent)
 
         # Some events should not be triggered during undo/redo
         # such as line stripping
@@ -1522,12 +1520,9 @@ def sort_key(completion):
 
             self.completion_widget.show_list(
                 completion_list, position, automatic)
-
-            self.kite_call_to_action.handle_processed_completions(completions)
         except RuntimeError:
             # This is triggered when a codeeditor instance was removed
             # before the response can be processed.
-            self.kite_call_to_action.hide_coverage_cta()
             return
         except Exception:
             self.log_lsp_handle_errors('Error when processing completions')
@@ -4612,8 +4607,6 @@ def keyPressEvent(self, event):
         event.ignore()
         self.sig_key_pressed.emit(event)
 
-        self.kite_call_to_action.handle_key_press(event)
-
         key = event.key()
         text = to_text_string(event.text())
         has_selection = self.has_selected_text()
@@ -5304,7 +5297,6 @@ def leaveEvent(self, event):
     def mousePressEvent(self, event):
         """Override Qt method."""
         self.hide_tooltip()
-        self.kite_call_to_action.handle_mouse_press(event)
 
         ctrl = event.modifiers() & Qt.ControlModifier
         alt = event.modifiers() & Qt.AltModifier
diff --git a/spyder/plugins/editor/widgets/editor.py b/spyder/plugins/editor/widgets/editor.py
index 5b72d994f92..68952315162 100644
--- a/spyder/plugins/editor/widgets/editor.py
+++ b/spyder/plugins/editor/widgets/editor.py
@@ -1636,7 +1636,13 @@ def close_file(self, index=None, force=False):
 
             filename = self.data[index].filename
             self.remove_from_data(index)
-            finfo.editor.notify_close()
+            editor = finfo.editor
+            editor.notify_close()
+            editor.setParent(None)
+            editor.completion_widget.setParent(None)
+            if self.parent():
+                # Can be None in tests
+                self.get_plugin().unregister_widget_shortcuts(editor)
 
             # We pass self object ID as a QString, because otherwise it would
             # depend on the platform: long for 64bit, int for 32bit. Replacing
diff --git a/spyder/plugins/editor/widgets/tests/test_editorsplitter.py b/spyder/plugins/editor/widgets/tests/test_editorsplitter.py
index 51503cefdcd..558c21dcdc5 100644
--- a/spyder/plugins/editor/widgets/tests/test_editorsplitter.py
+++ b/spyder/plugins/editor/widgets/tests/test_editorsplitter.py
@@ -70,12 +70,10 @@ def register_editorstack(editorstack):
         editorstack.register_completion_capabilities(capabilities, 'python')
 
     def clone(editorstack, template=None):
-        # editorstack.clone_from(template)
-        editor_stack = EditorStack(None, [])
-        editor_stack.set_find_widget(Mock())
-        editor_stack.set_io_actions(Mock(), Mock(), Mock(), Mock())
+        editorstack.set_find_widget(Mock())
+        editorstack.set_io_actions(Mock(), Mock(), Mock(), Mock())
         # Emulate "cloning"
-        editorsplitter.editorstack.new('test.py', 'utf-8', text)
+        editorstack.new('test.py', 'utf-8', text)
 
     mock_plugin = Mock()
     editorsplitter = EditorSplitter(
diff --git a/spyder/plugins/ipythonconsole/plugin.py b/spyder/plugins/ipythonconsole/plugin.py
index 17df1a897a5..45d90a522f5 100644
--- a/spyder/plugins/ipythonconsole/plugin.py
+++ b/spyder/plugins/ipythonconsole/plugin.py
@@ -392,7 +392,7 @@ def update_font(self):
     def on_close(self, cancelable=False):
         """Perform actions when plugin is closed"""
         self.get_widget().mainwindow_close = True
-        return self.get_widget().close_clients()
+        return self.get_widget().close_all_clients()
 
     def on_mainwindow_visible(self):
         self.create_new_client(give_focus=False)
diff --git a/spyder/plugins/ipythonconsole/tests/test_ipythonconsole.py b/spyder/plugins/ipythonconsole/tests/test_ipythonconsole.py
index ec16b524c0b..2ebf1417833 100644
--- a/spyder/plugins/ipythonconsole/tests/test_ipythonconsole.py
+++ b/spyder/plugins/ipythonconsole/tests/test_ipythonconsole.py
@@ -1282,26 +1282,27 @@ def test_set_elapsed_time(ipyconsole, qtbot):
     client = ipyconsole.get_current_client()
 
     # Show time label.
-    ipyconsole.get_widget().set_show_elapsed_time_current_client(True)
+    main_widget = ipyconsole.get_widget()
+    main_widget.set_show_elapsed_time_current_client(True)
 
     # Set time to 2 minutes ago.
     client.t0 -= 120
     with qtbot.waitSignal(client.timer.timeout, timeout=5000):
         ipyconsole.get_widget().set_client_elapsed_time(client)
-    assert ('00:02:00' in client.time_label.text() or
-            '00:02:01' in client.time_label.text())
+    assert ('00:02:00' in main_widget.time_label.text() or
+            '00:02:01' in main_widget.time_label.text())
 
     # Wait for a second to pass, to ensure timer is counting up
     with qtbot.waitSignal(client.timer.timeout, timeout=5000):
         pass
-    assert ('00:02:01' in client.time_label.text() or
-            '00:02:02' in client.time_label.text())
+    assert ('00:02:01' in main_widget.time_label.text() or
+            '00:02:02' in main_widget.time_label.text())
 
     # Make previous time later than current time.
     client.t0 += 2000
     with qtbot.waitSignal(client.timer.timeout, timeout=5000):
         pass
-    assert '00:00:00' in client.time_label.text()
+    assert '00:00:00' in main_widget.time_label.text()
 
     client.timer.timeout.disconnect(client.show_time)
 
diff --git a/spyder/plugins/ipythonconsole/widgets/client.py b/spyder/plugins/ipythonconsole/widgets/client.py
index 846f84497f4..5978d121cd3 100644
--- a/spyder/plugins/ipythonconsole/widgets/client.py
+++ b/spyder/plugins/ipythonconsole/widgets/client.py
@@ -81,6 +81,7 @@ class ClientWidget(QWidget, SaveHistoryMixin, SpyderWidgetMixin):
 
     sig_append_to_history_requested = Signal(str, str)
     sig_execution_state_changed = Signal()
+    sig_time_label = Signal(str)
 
     CONF_SECTION = 'ipython_console'
     SEPARATOR = '{0}## ---({1})---'.format(os.linesep*2, time.ctime())
@@ -98,7 +99,6 @@ def __init__(self, parent, id_,
                  given_name=None,
                  give_focus=True,
                  options_button=None,
-                 time_label=None,
                  show_elapsed_time=False,
                  reset_warning=True,
                  ask_before_restart=True,
@@ -126,7 +126,6 @@ def __init__(self, parent, id_,
 
         # --- Other attrs
         self.context_menu_actions = context_menu_actions
-        self.time_label = time_label
         self.options_button = options_button
         self.history = []
         self.allow_rename = True
@@ -644,6 +643,25 @@ def set_color_scheme(self, color_scheme, reset=True):
         except AttributeError:
             pass
 
+    def close_client(self, is_last_client):
+        """Close the client."""
+        # Needed to handle a RuntimeError. See spyder-ide/spyder#5568.
+        try:
+            # Close client
+            self.stop_button_click_handler()
+        except RuntimeError:
+            pass
+
+        # Disconnect timer needed to update elapsed time
+        try:
+            self.timer.timeout.disconnect(self.show_time)
+        except (RuntimeError, TypeError):
+            pass
+
+        self.shutdown(is_last_client)
+        self.close()
+        self.setParent(None)
+
     def shutdown(self, is_last_client):
         """Shutdown connection and kernel if needed."""
         self.dialog_manager.close_all()
@@ -899,8 +917,6 @@ def show_env(self, env):
 
     def show_time(self, end=False):
         """Text to show in time_label."""
-        if self.time_label is None:
-            return
 
         elapsed_time = time.monotonic() - self.t0
         # System time changed to past date, so reset start.
@@ -919,9 +935,9 @@ def show_time(self, end=False):
                "</b></span>" % (color,
                                 time.strftime(fmt, time.gmtime(elapsed_time)))
         if self.show_elapsed_time:
-            self.time_label.setText(text)
+            self.sig_time_label.emit(text)
         else:
-            self.time_label.setText("")
+            self.sig_time_label.emit("")
 
     @Slot(bool)
     def set_show_elapsed_time(self, state):
diff --git a/spyder/plugins/ipythonconsole/widgets/debugging.py b/spyder/plugins/ipythonconsole/widgets/debugging.py
index 695b9ce3287..dc456ffd0d8 100644
--- a/spyder/plugins/ipythonconsole/widgets/debugging.py
+++ b/spyder/plugins/ipythonconsole/widgets/debugging.py
@@ -10,6 +10,7 @@
 """
 
 # Standard library imports
+import atexit
 import pdb
 import re
 
@@ -220,6 +221,8 @@ def shutdown(self):
         if self._pdb_history_file is not None:
             try:
                 self._pdb_history_file.save_thread.stop()
+                # Now that it was called, no need to call it at exit
+                atexit.unregister(self._pdb_history_file.save_thread.stop)
             except AttributeError:
                 pass
 
diff --git a/spyder/plugins/ipythonconsole/widgets/main_widget.py b/spyder/plugins/ipythonconsole/widgets/main_widget.py
index ada17eeb05e..c4a22e4595f 100644
--- a/spyder/plugins/ipythonconsole/widgets/main_widget.py
+++ b/spyder/plugins/ipythonconsole/widgets/main_widget.py
@@ -401,7 +401,7 @@ def __init__(self, name=None, plugin=None, parent=None):
 
     def on_close(self):
         self.mainwindow_close = True
-        self.close_clients()
+        self.close_all_clients()
 
     # ---- PluginMainWidget API and settings handling
     # ------------------------------------------------------------------------
@@ -1436,7 +1436,6 @@ def create_new_client(self, give_focus=True, filename='', is_cython=False,
                               interpreter_versions=self.interpreter_versions(),
                               connection_file=cf,
                               context_menu_actions=self.context_menu_actions,
-                              time_label=self.time_label,
                               show_elapsed_time=show_elapsed_time,
                               reset_warning=reset_warning,
                               given_name=given_name,
@@ -1575,7 +1574,6 @@ def create_client_for_kernel(self, connection_file, hostname, sshkey,
                               interpreter_versions=self.interpreter_versions(),
                               connection_file=connection_file,
                               context_menu_actions=self.context_menu_actions,
-                              time_label=self.time_label,
                               hostname=hostname,
                               is_external_kernel=is_external_kernel,
                               is_spyder_kernel=known_spyder_kernel,
@@ -1865,6 +1863,9 @@ def register_client(self, client, give_focus=True):
         # Connect client execution state to be reflected in the interface
         client.sig_execution_state_changed.connect(self.update_actions)
 
+        # Show time label
+        client.sig_time_label.connect(self.time_label.setText)
+
     def close_client(self, index=None, client=None, ask_recursive=True):
         """Close client tab from index or widget (or close current tab)"""
         if not self.tabwidget.count():
@@ -1883,19 +1884,6 @@ def close_client(self, index=None, client=None, ask_recursive=True):
         if index is not None:
             client = self.tabwidget.widget(index)
 
-        # Needed to handle a RuntimeError. See spyder-ide/spyder#5568.
-        try:
-            # Close client
-            client.stop_button_click_handler()
-        except RuntimeError:
-            pass
-
-        # Disconnect timer needed to update elapsed time
-        try:
-            client.timer.timeout.disconnect(client.show_time)
-        except (RuntimeError, TypeError):
-            pass
-
         # Check if related clients or kernels are opened
         # and eventually ask before closing them
         if not self.mainwindow_close and ask_recursive:
@@ -1919,13 +1907,11 @@ def close_client(self, index=None, client=None, ask_recursive=True):
             if close_all == QMessageBox.Yes:
                 self.close_related_clients(client)
 
-        last_client = len(self.get_related_clients(client)) == 0
-        client.shutdown(last_client)
-        client.close()
-
         # Note: client index may have changed after closing related widgets
         self.tabwidget.removeTab(self.tabwidget.indexOf(client))
         self.clients.remove(client)
+        is_last_client = len(self.get_related_clients(client)) == 0
+        client.close_client(is_last_client)
 
         # This is needed to prevent that hanged consoles make reference
         # to an index that doesn't exist. See spyder-ide/spyder#4881
@@ -1940,7 +1926,7 @@ def close_client(self, index=None, client=None, ask_recursive=True):
         if not self.tabwidget.count() and self.create_new_client_if_empty:
             self.create_new_client()
 
-    def close_clients(self):
+    def close_all_clients(self):
         """
         Perform close actions for each running client.
 
@@ -1949,17 +1935,16 @@ def close_clients(self):
         bool
             If the closing action was succesful.
         """
-        open_clients = self.clients.copy()
-        for client in self.clients:
-            last_client = (
-                len(self.get_related_clients(client, open_clients)) == 0)
-            client.shutdown(last_client)
-            client.close()
-            open_clients.remove(client)
+        while self.clients:
+            client = self.clients.pop()
+            is_last_client = len(self.get_related_clients(client)) == 0
+            client.close_client(is_last_client)
+
         # Close all closing shellwidgets.
         ShellWidget.wait_all_shutdown()
         # Close cached kernel
         self.close_cached_kernel()
+        self.filenames = []
         return True
 
     def get_client_index_from_id(self, client_id):
diff --git a/spyder/plugins/outlineexplorer/widgets.py b/spyder/plugins/outlineexplorer/widgets.py
index 3d5ddf4391a..bce7680e4d8 100644
--- a/spyder/plugins/outlineexplorer/widgets.py
+++ b/spyder/plugins/outlineexplorer/widgets.py
@@ -347,14 +347,15 @@ def toggle_fullpath_mode(self, state):
     @on_conf_change(option='show_all_files')
     def toggle_show_all_files(self, state):
         self.show_all_files = state
-        if self.current_editor is not None:
-            editor_id = self.editor_ids[self.current_editor]
+        current_editor = self.current_editor
+        if current_editor is not None:
+            editor_id = self.editor_ids[current_editor]
             item = self.editor_items[editor_id].node
             self.__hide_or_show_root_items(item)
             self.__sort_toplevel_items()
             if self.show_all_files is False:
                 self.root_item_selected(
-                    self.editor_items[self.editor_ids[self.current_editor]])
+                    self.editor_items[self.editor_ids[current_editor]])
             self.do_follow_cursor()
 
     @on_conf_change(option='show_comments')
diff --git a/spyder/plugins/plots/widgets/main_widget.py b/spyder/plugins/plots/widgets/main_widget.py
index 03dfb172470..6cd826b18fe 100644
--- a/spyder/plugins/plots/widgets/main_widget.py
+++ b/spyder/plugins/plots/widgets/main_widget.py
@@ -308,6 +308,7 @@ def create_new_widget(self, shellwidget):
 
     def close_widget(self, fig_browser):
         fig_browser.close()
+        fig_browser.setParent(None)
 
     def switch_widget(self, fig_browser, old_fig_browser):
         option_keys = [('auto_fit_plotting', True),
diff --git a/spyder/plugins/variableexplorer/widgets/main_widget.py b/spyder/plugins/variableexplorer/widgets/main_widget.py
index 3a945fdb837..8d0687cf820 100644
--- a/spyder/plugins/variableexplorer/widgets/main_widget.py
+++ b/spyder/plugins/variableexplorer/widgets/main_widget.py
@@ -484,6 +484,7 @@ def create_new_widget(self, shellwidget):
 
     def close_widget(self, nsb):
         nsb.close()
+        nsb.setParent(None)
 
     def import_data(self, filenames=None):
         """