diff --git a/lib/galaxy/managers/notification.py b/lib/galaxy/managers/notification.py
index 55008a4ceef4..243b68eed12a 100644
--- a/lib/galaxy/managers/notification.py
+++ b/lib/galaxy/managers/notification.py
@@ -275,8 +275,8 @@ def update_broadcasted_notification(self, notification_id: int, request: Notific
     def get_user_notification_preferences(self, user: User) -> UserNotificationPreferences:
         """Gets the user's current notification preferences or the default ones if no preferences are set."""
         current_notification_preferences = (
-            user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME]
-            if NOTIFICATION_PREFERENCES_SECTION_NAME in user.preferences
+            user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME]  # type:ignore[index]
+            if NOTIFICATION_PREFERENCES_SECTION_NAME in user.preferences  # type:ignore[operator]
             else None
         )
         try:
@@ -291,7 +291,7 @@ def update_user_notification_preferences(
         """Updates the user's notification preferences with the requested changes."""
         notification_preferences = self.get_user_notification_preferences(user)
         notification_preferences.update(request.preferences)
-        user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME] = notification_preferences.json()
+        user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME] = notification_preferences.json()  # type:ignore[index]
         with transaction(self.sa_session):
             self.sa_session.commit()
         return notification_preferences
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 8bbc703056b0..d19a55288fc6 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -1765,7 +1765,7 @@ def __module_from_dict(
         temp_input_connections: Dict[str, Union[List[DictConnection], DictConnection]] = step_dict.get(
             "input_connections", {}
         )
-        step.temp_input_connections = temp_input_connections
+        step.temp_input_connections = temp_input_connections  # type: ignore[assignment]
 
         # Create the model class for the step
         steps.append(step)
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 2ff8fe290e0b..4721ce682c09 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -1378,7 +1378,7 @@ def get_inputs(self):
 
     def restrict_options(self, step, connections: Iterable[WorkflowStepConnection], default_value):
         try:
-            static_options = []
+            static_options = []  # type:ignore[var-annotated]
             # Retrieve possible runtime options for 'select' type inputs
             for connection in connections:
                 # Well this isn't a great assumption...
@@ -2511,13 +2511,13 @@ def inject(self, step: WorkflowStep, step_args=None, steps=None, **kwargs):
         If step_args is provided from a web form this is applied to generate
         'state' else it is just obtained from the database.
         """
-        step.upgrade_messages = {}
+        step.upgrade_messages = {}  # type: ignore[assignment]
 
         # Make connection information available on each step by input name.
         step.setup_input_connections_by_name()
 
         # Populate module.
-        module = step.module = module_factory.from_workflow_step(self.trans, step, **kwargs)
+        module = step.module = module_factory.from_workflow_step(self.trans, step, **kwargs)  # type: ignore[assignment]
 
         # Any connected input needs to have value DummyDataset (these
         # are not persisted so we need to do it every time)
diff --git a/test/unit/app/tools/test_metadata.py b/test/unit/app/tools/test_metadata.py
index 8f83c6b90ef6..7e1784a84caa 100644
--- a/test/unit/app/tools/test_metadata.py
+++ b/test/unit/app/tools/test_metadata.py
@@ -18,7 +18,7 @@ class TestMetadata(TestCase, tools_support.UsesTools):
     def setUp(self):
         super().setUp()
         self.setup_app()
-        model.Dataset.object_store = self.app.object_store
+        model.Dataset.object_store = self.app.object_store  # type: ignore[assignment]
         job = model.Job()
         sa_session = self.app.model.session
         sa_session.add(job)