diff --git a/spyder/plugins/application/container.py b/spyder/plugins/application/container.py
index f3dd0d7a43b..86e1d2029db 100644
--- a/spyder/plugins/application/container.py
+++ b/spyder/plugins/application/container.py
@@ -15,8 +15,8 @@
 import sys
 
 # Third party imports
-from qtpy.QtCore import Qt, QThread, Slot
-from qtpy.QtWidgets import QMessageBox, QAction
+from qtpy.QtCore import Qt, QThread, QTimer, Slot
+from qtpy.QtWidgets import QAction, QMessageBox
 
 # Local imports
 from spyder import (
@@ -24,7 +24,6 @@
 from spyder import dependencies
 from spyder.api.translations import get_translation
 from spyder.api.widgets.main_container import PluginMainContainer
-from spyder.config.base import DEV
 from spyder.config.utils import is_anaconda
 from spyder.utils.qthelpers import start_file, DialogManager
 from spyder.widgets.about import AboutDialog
@@ -64,7 +63,11 @@ class ApplicationActions:
 
 
 class ApplicationContainer(PluginMainContainer):
+
     def setup(self):
+        # Compute dependencies in a thread to not block the interface.
+        self.dependencies_thread = QThread()
+
         # Attributes
         self.dialog_manager = DialogManager()
         self.give_updates_feedback = False
@@ -142,11 +145,6 @@ def setup(self):
             shortcut_context="_",
             register_shortcut=True)
 
-        # Initialize
-        if DEV is None and self.get_conf('check_updates_on_startup'):
-            self.give_updates_feedback = False
-            self.check_updates(startup=True)
-
     def update_actions(self):
         pass
 
@@ -174,6 +172,7 @@ def _check_updates_ready(self):
         box = MessageCheckBox(icon=QMessageBox.Information,
                               parent=self)
         box.setWindowTitle(_("New Spyder version"))
+        box.setAttribute(Qt.WA_ShowWithoutActivating)
         box.set_checkbox_text(_("Check for updates at startup"))
         box.setStandardButtons(QMessageBox.Ok)
         box.setDefaultButton(QMessageBox.Ok)
@@ -216,7 +215,7 @@ def _check_updates_ready(self):
                 msg = header + content + footer
                 box.setText(msg)
                 box.set_check_visible(True)
-                box.exec_()
+                box.show()
                 check_updates = box.is_checked()
             elif feedback:
                 msg = _("Spyder is up to date.")
@@ -249,7 +248,15 @@ def check_updates(self, startup=False):
         self.worker_updates.sig_ready.connect(self.thread_updates.quit)
         self.worker_updates.moveToThread(self.thread_updates)
         self.thread_updates.started.connect(self.worker_updates.start)
-        self.thread_updates.start()
+
+        # Delay starting this check to avoid blocking the main window
+        # while loading.
+        # Fixes spyder-ide/spyder#15839
+        updates_timer = QTimer(self)
+        updates_timer.setInterval(3000)
+        updates_timer.setSingleShot(True)
+        updates_timer.timeout.connect(self.thread_updates.start)
+        updates_timer.start()
 
     @Slot()
     def show_dependencies(self):
@@ -271,7 +278,16 @@ def show_windows_env_variables(self):
 
     def compute_dependencies(self):
         """Compute dependencies"""
-        dependencies.declare_dependencies()
+        self.dependencies_thread.run = dependencies.declare_dependencies
+        self.dependencies_thread.finished.connect(
+            self.report_missing_dependencies)
+
+        # This avoids computing missing deps before the window is fully up
+        dependencies_timer = QTimer(self)
+        dependencies_timer.setInterval(10000)
+        dependencies_timer.setSingleShot(True)
+        dependencies_timer.timeout.connect(self.dependencies_thread.start)
+        dependencies_timer.start()
 
     @Slot()
     def report_missing_dependencies(self):
@@ -304,6 +320,7 @@ def report_missing_dependencies(self):
             message_box = QMessageBox(self)
             message_box.setIcon(QMessageBox.Critical)
             message_box.setAttribute(Qt.WA_DeleteOnClose)
+            message_box.setAttribute(Qt.WA_ShowWithoutActivating)
             message_box.setStandardButtons(QMessageBox.Ok)
             message_box.setWindowModality(Qt.NonModal)
             message_box.setWindowTitle(_('Error'))
diff --git a/spyder/plugins/application/plugin.py b/spyder/plugins/application/plugin.py
index 1a9877a0dbd..662db07f7d7 100644
--- a/spyder/plugins/application/plugin.py
+++ b/spyder/plugins/application/plugin.py
@@ -14,7 +14,7 @@
 import sys
 
 # Third party imports
-from qtpy.QtCore import Qt, QThread, QTimer, Slot
+from qtpy.QtCore import Slot
 from qtpy.QtWidgets import QMenu
 
 # Local imports
@@ -43,12 +43,6 @@ class Application(SpyderPluginV2):
     CONF_FILE = False
     CONF_WIDGET_CLASS = ApplicationConfigPage
 
-    def __init__(self, parent, configuration=None):
-        super().__init__(parent, configuration)
-
-        # Compute dependencies in a thread to not block the interface.
-        self.dependencies_thread = QThread()
-
     def get_name(self):
         return _('Application')
 
@@ -92,23 +86,19 @@ def on_close(self):
 
     def on_mainwindow_visible(self):
         """Actions after the mainwindow in visible."""
+        container = self.get_container()
+
         # Show dialog with missing dependencies
         if not running_under_pytest():
-            container = self.get_container()
-            self.dependencies_thread.run = container.compute_dependencies
-            self.dependencies_thread.finished.connect(
-                container.report_missing_dependencies)
-
-            # This avoids computing missing deps before the window is fully up
-            dependencies_timer = QTimer(self)
-            dependencies_timer.setInterval(10000)
-            dependencies_timer.setSingleShot(True)
-            dependencies_timer.timeout.connect(self.dependencies_thread.start)
-            dependencies_timer.start()
-
-    # --- Private methods
-    # ------------------------------------------------------------------------
+            container.compute_dependencies()
+
+        # Check for updates
+        if DEV is None and self.get_conf('check_updates_on_startup'):
+            container.give_updates_feedback = False
+            container.check_updates(startup=True)
 
+    # ---- Private methods
+    # ------------------------------------------------------------------------
     def _populate_file_menu(self):
         mainmenu = self.get_plugin(Plugins.MainMenu)
         if mainmenu:
@@ -172,7 +162,7 @@ def _populate_help_menu_about_section(self, mainmenu):
                 menu_id=ApplicationMenus.Help,
                 section=HelpMenuSections.About)
 
-    # --- Public API
+    # ---- Public API
     # ------------------------------------------------------------------------
     def get_application_context_menu(self, parent=None):
         """
diff --git a/spyder/plugins/ipythonconsole/widgets/shell.py b/spyder/plugins/ipythonconsole/widgets/shell.py
index 55be657ab5b..d8125d10bc4 100644
--- a/spyder/plugins/ipythonconsole/widgets/shell.py
+++ b/spyder/plugins/ipythonconsole/widgets/shell.py
@@ -480,7 +480,7 @@ def reset_namespace(self, warning=False, message=False):
             box.set_check_visible(True)
             box.setText(warn_str)
 
-            answer = box.exec_()
+            answer = box.show()
 
             # Update checkbox based on user interaction
             self.set_conf(
diff --git a/spyder/widgets/helperwidgets.py b/spyder/widgets/helperwidgets.py
index f2706c765b1..2a04be3c9d9 100644
--- a/spyder/widgets/helperwidgets.py
+++ b/spyder/widgets/helperwidgets.py
@@ -67,7 +67,8 @@ class MessageCheckBox(QMessageBox):
     def __init__(self, *args, **kwargs):
         super(MessageCheckBox, self).__init__(*args, **kwargs)
 
-        self._checkbox = QCheckBox()
+        self.setWindowModality(Qt.NonModal)
+        self._checkbox = QCheckBox(self)
 
         # Set layout to include checkbox
         size = 9