diff --git a/plinth/package.py b/plinth/package.py
index a7dbcb734..c03223eb4 100644
--- a/plinth/package.py
+++ b/plinth/package.py
@@ -9,6 +9,7 @@ import logging
 import pathlib
 import subprocess
 import threading
+import time
 from typing import Optional, Union
 
 import apt.cache
@@ -403,6 +404,13 @@ def install(package_names, skip_recommends=False, force_configuration=None,
 
         return
 
+    start_time = time.time()
+    while is_package_manager_busy():
+        if time.time() - start_time >= 24 * 3600:  # One day
+            raise PackageException(_('Timeout waiting for package manager'))
+
+        time.sleep(3)  # seconds
+
     logger.info('Running install for app - %s, packages - %s',
                 operation.app_id, package_names)
 
diff --git a/plinth/setup.py b/plinth/setup.py
index 718127465..510ea8591 100644
--- a/plinth/setup.py
+++ b/plinth/setup.py
@@ -176,10 +176,6 @@ def _run_first_setup():
 
 def _run_regular_setup():
     """Run setup on all apps also installing required packages."""
-    # TODO show notification that upgrades are running
-    if package.is_package_manager_busy():
-        raise Exception('Package manager is busy.')
-
     app_ids = _get_apps_for_regular_setup()
     run_setup_on_apps(app_ids, allow_install=True)
 
diff --git a/plinth/templates/setup.html b/plinth/templates/setup.html
index 6895ddfa6..77501a018 100644
--- a/plinth/templates/setup.html
+++ b/plinth/templates/setup.html
@@ -34,14 +34,7 @@
     <form class="form-install" action="" method="post">
       {% csrf_token %}
 
-      {% if package_manager_is_busy %}
-        <div class="alert alert-warning" role="alert">
-          {% blocktrans trimmed %}
-            Another installation or upgrade is already running.
-            Please wait for a few moments before trying again.
-          {% endblocktrans %}
-        </div>
-      {% elif has_unavailable_packages %}
+      {% if has_unavailable_packages %}
         <div class="alert alert-warning" role="alert">
           {% blocktrans trimmed %}
             This application is currently not available in your distribution.
@@ -64,7 +57,7 @@
       {% endif %}
 
       <input type="submit" class="btn btn-md btn-primary" name="install"
-             {% if package_manager_is_busy or has_unavailable_packages %}
+             {% if has_unavailable_packages %}
              disabled="disabled"
              {% endif %}
              {% if setup_state.value == 'needs-setup' %}
diff --git a/plinth/views.py b/plinth/views.py
index 3f85a804d..6310005af 100644
--- a/plinth/views.py
+++ b/plinth/views.py
@@ -287,8 +287,6 @@ class SetupView(TemplateView):
 
         # Perform expensive operation only if needed.
         if not context['operations']:
-            context[
-                'package_manager_is_busy'] = package.is_package_manager_busy()
             context[
                 'has_unavailable_packages'] = self._has_unavailable_packages(
                     app)