diff --git a/aiida/storage/psql_dos/migrator.py b/aiida/storage/psql_dos/migrator.py
index b48ae7fded..cc5e11efa5 100644
--- a/aiida/storage/psql_dos/migrator.py
+++ b/aiida/storage/psql_dos/migrator.py
@@ -384,6 +384,7 @@ def migrate(self) -> None:
         # finally migrate to the main head revision
         MIGRATE_LOGGER.report('Migrating to the head of the main branch')
         self.migrate_up('main@head')
+        self.connection.commit()
 
     def migrate_up(self, version: str) -> None:
         """Migrate the database up to a specific version.
diff --git a/tests/storage/psql_dos/migrations/test_all_schema.py b/tests/storage/psql_dos/migrations/test_all_schema.py
index 40dedae7a7..3b57d0e687 100644
--- a/tests/storage/psql_dos/migrations/test_all_schema.py
+++ b/tests/storage/psql_dos/migrations/test_all_schema.py
@@ -21,6 +21,27 @@ def test_main(version, uninitialised_profile, reflect_schema, data_regression):
     data_regression.check(reflect_schema(uninitialised_profile))
 
 
+def test_main_initialized(uninitialised_profile):
+    """Test that ``migrate`` properly stamps the new schema version when updating database with existing schema."""
+    migrator = PsqlDosMigrator(uninitialised_profile)
+
+    # Initialize database at first version of main branch
+    migrator.migrate_up('main@main_0001')
+    assert migrator.get_schema_version_profile(check_legacy=False) == 'main_0001'
+    migrator.close()
+
+    # Reinitialize the migrator to make sure we are fetching actual state of database and not in-memory state and then
+    # migrate to head schema version.
+    migrator = PsqlDosMigrator(uninitialised_profile)
+    migrator.migrate()
+    migrator.close()
+
+    # Reinitialize the migrator to make sure we are fetching actual state of database and not in-memory state and then
+    # assert that the database version is properly set to the head schema version
+    migrator = PsqlDosMigrator(uninitialised_profile)
+    assert migrator.get_schema_version_profile(check_legacy=False) == migrator.get_schema_version_head()
+
+
 def test_head_vs_orm(uninitialised_profile, reflect_schema, data_regression):
     """Test that the migrations produce the same database schema as the models."""
     migrator = PsqlDosMigrator(uninitialised_profile)