diff --git a/app/commands.py b/app/commands.py
index 5580e7632..c88e2bcb3 100644
--- a/app/commands.py
+++ b/app/commands.py
@@ -12,7 +12,7 @@ from click_datetime import Datetime as click_dt
 from faker import Faker
 from flask import current_app, json
 from notifications_python_client.authentication import create_jwt_token
-from sqlalchemy import and_, text
+from sqlalchemy import and_, select, text, update
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.orm.exc import NoResultFound
 
@@ -123,8 +123,8 @@ def purge_functional_test_data(user_email_prefix):
     if getenv("NOTIFY_ENVIRONMENT", "") not in ["development", "test"]:
         current_app.logger.error("Can only be run in development")
         return
-
-    users = User.query.filter(User.email_address.like(f"{user_email_prefix}%")).all()
+    stmt = select(User).where(User.email_address.like(f"{user_email_prefix}%"))
+    users = db.session.execute(stmt).scalars().all()
     for usr in users:
         # Make sure the full email includes a uuid in it
         # Just in case someone decides to use a similar email address.
@@ -338,9 +338,10 @@ def populate_organizations_from_file(file_name):
             email_branding = None
             email_branding_column = columns[5].strip()
             if len(email_branding_column) > 0:
-                email_branding = EmailBranding.query.filter(
+                stmt = select(EmailBranding).where(
                     EmailBranding.name == email_branding_column
-                ).one()
+                )
+                email_branding = db.session.execute(stmt).scalars().one()
             data = {
                 "name": columns[0],
                 "active": True,
@@ -406,10 +407,14 @@ def populate_organization_agreement_details_from_file(file_name):
 
 @notify_command(name="associate-services-to-organizations")
 def associate_services_to_organizations():
-    services = Service.get_history_model().query.filter_by(version=1).all()
+    stmt = select(Service.get_history_model()).where(
+        Service.get_history_model().version == 1
+    )
+    services = db.session.execute(stmt).scalars().all()
 
     for s in services:
-        created_by_user = User.query.filter_by(id=s.created_by_id).first()
+        stmt = select(User).where(User.id == s.created_by_id)
+        created_by_user = db.session.execute(stmt).scalars().first()
         organization = dao_get_organization_by_email_address(
             created_by_user.email_address
         )
@@ -467,15 +472,16 @@ def populate_go_live(file_name):
 
 @notify_command(name="fix-billable-units")
 def fix_billable_units():
-    query = Notification.query.filter(
+    stmt = select(Notification).where(
         Notification.notification_type == NotificationType.SMS,
         Notification.status != NotificationStatus.CREATED,
         Notification.sent_at == None,  # noqa
         Notification.billable_units == 0,
         Notification.key_type != KeyType.TEST,
     )
+    all = db.session.execute(stmt).scalars().all()
 
-    for notification in query.all():
+    for notification in all:
         template_model = dao_get_template_by_id(
             notification.template_id, notification.template_version
         )
@@ -490,9 +496,12 @@ def fix_billable_units():
             f"Updating notification: {notification.id} with {template.fragment_count} billable_units"
         )
 
-        Notification.query.filter(Notification.id == notification.id).update(
-            {"billable_units": template.fragment_count}
+        stmt = (
+            update(Notification)
+            .where(Notification.id == notification.id)
+            .values({"billable_units": template.fragment_count})
         )
+        db.session.execute(stmt)
     db.session.commit()
     current_app.logger.info("End fix_billable_units")
 
@@ -637,8 +646,8 @@ def populate_annual_billing_with_defaults(year, missing_services_only):
     This is useful to ensure all services start the new year with the correct annual billing.
     """
     if missing_services_only:
-        active_services = (
-            Service.query.filter(Service.active)
+        stmt = (
+            select(Service)
             .outerjoin(
                 AnnualBilling,
                 and_(
@@ -646,20 +655,18 @@ def populate_annual_billing_with_defaults(year, missing_services_only):
                     AnnualBilling.financial_year_start == year,
                 ),
             )
-            .filter(AnnualBilling.id == None)  # noqa
-            .all()
+            .where(Service.active, AnnualBilling.id == None)  # noqa
         )
+        active_services = db.session.execute(stmt).scalars().all()
     else:
-        active_services = Service.query.filter(Service.active).all()
+        stmt = select(Service).where(Service.active)
+        active_services = db.session.execute(stmt).scalars().all()
     previous_year = year - 1
-    services_with_zero_free_allowance = (
-        db.session.query(AnnualBilling.service_id)
-        .filter(
-            AnnualBilling.financial_year_start == previous_year,
-            AnnualBilling.free_sms_fragment_limit == 0,
-        )
-        .all()
+    stmt = select(AnnualBilling.id).where(
+        AnnualBilling.financial_year_start == previous_year,
+        AnnualBilling.free_sms_fragment_limit == 0,
     )
+    services_with_zero_free_allowance = db.session.execute(stmt).scalars().all()
 
     for service in active_services:
         # If a service has free_sms_fragment_limit for the previous year
@@ -750,7 +757,8 @@ def create_user_jwt(token):
 
 
 def _update_template(id, name, template_type, content, subject):
-    template = Template.query.filter_by(id=id).first()
+    stmt = select(Template).where(Template.id == id)
+    template = db.session.execute(stmt).scalars().first()
     if not template:
         template = Template(id=id)
         template.service_id = "d6aa2c68-a2d9-4437-ab19-3ae8eb202553"
@@ -761,7 +769,8 @@ def _update_template(id, name, template_type, content, subject):
     template.content = "\n".join(content)
     template.subject = subject
 
-    history = TemplateHistory.query.filter_by(id=id).first()
+    stmt = select(TemplateHistory).where(TemplateHistory.id == id)
+    history = db.session.execute(stmt).scalars().first()
     if not history:
         history = TemplateHistory(id=id)
         history.service_id = "d6aa2c68-a2d9-4437-ab19-3ae8eb202553"