diff --git a/easybuild/easyblocks/generic/pythonbundle.py b/easybuild/easyblocks/generic/pythonbundle.py
index feb52cddfe..b1a3fe37d2 100644
--- a/easybuild/easyblocks/generic/pythonbundle.py
+++ b/easybuild/easyblocks/generic/pythonbundle.py
@@ -151,10 +151,12 @@ def sanity_check_step(self, *args, **kwargs):
         """Custom sanity check for bundle of Python package."""
 
         if self.pylibdir is None:
-            # Python attributes not set up yet, happens e.g. with --sanity-check-only
-            # Load module first to get the right python command
-            self.fake_mod_data = self.sanity_check_load_module(extension=kwargs.get('extension', False),
-                                                               extra_modules=kwargs.get('extra_modules', None))
+            # Python attributes not set up yet, happens e.g. with --sanity-check-only, so do it now.
+            # This also ensures the exts_filter option for extensions is set correctly.
+            # Load module first to get the right python command.
+            if not self.sanity_check_module_loaded:
+                self.fake_mod_data = self.sanity_check_load_module(extension=kwargs.get('extension', False),
+                                                                   extra_modules=kwargs.get('extra_modules', None))
             self.prepare_python()
 
         # inject directory path that uses %(pyshortver)s template into default value for sanity_check_paths
@@ -168,9 +170,16 @@ def sanity_check_step(self, *args, **kwargs):
 
         super(Bundle, self).sanity_check_step(*args, **kwargs)
 
-        # After the super-call self.ext_instances is initialized, so we can check the extensions
+    def _sanity_check_step_extensions(self):
+        """Run the pip check for extensions if enabled"""
+        super(PythonBundle, self)._sanity_check_step_extensions()
+
         sanity_pip_check = self.cfg['sanity_pip_check']
         unversioned_packages = set(self.cfg['unversioned_packages'])
+
+        # The options should be set in the main EC and cannot be different between extensions.
+        # For backwards compatibility and to avoid surprises enable the pip-check if it is enabled
+        # in the main EC or any extension and build the union of all unversioned_packages.
         has_sanity_pip_check_mismatch = False
         all_unversioned_packages = unversioned_packages.copy()
         for ext in self.ext_instances:
@@ -186,5 +195,6 @@ def sanity_check_step(self, *args, **kwargs):
         if all_unversioned_packages != unversioned_packages:
             self.log.deprecated('For bundles of PythonPackage the unversioned_packages option '
                                 'in the main EasyConfig must be used', '5.0')
+
         if sanity_pip_check:
             run_pip_check(self.log, self.python_cmd, all_unversioned_packages)
diff --git a/easybuild/easyblocks/generic/pythonpackage.py b/easybuild/easyblocks/generic/pythonpackage.py
index 396e66b1d8..d4dde65697 100644
--- a/easybuild/easyblocks/generic/pythonpackage.py
+++ b/easybuild/easyblocks/generic/pythonpackage.py
@@ -1035,10 +1035,10 @@ def sanity_check_step(self, *args, **kwargs):
         # load module early ourselves rather than letting parent sanity_check_step method do so,
         # since custom actions taken below require that environment is set up properly already
         # (especially when using --sanity-check-only)
-        if hasattr(self, 'sanity_check_module_loaded') and not self.sanity_check_module_loaded:
+        if not self.sanity_check_module_loaded:
             extension = self.is_extension or kwargs.get('extension', False)
             extra_modules = kwargs.get('extra_modules', None)
-            self.fake_mod_data = self.sanity_check_load_module(extension=extension, extra_modules=extra_modules)
+            self.sanity_check_load_module(extension=extension, extra_modules=extra_modules)
 
         # don't add user site directory to sys.path (equivalent to python -s)
         # see https://www.python.org/dev/peps/pep-0370/;