Maybe it is something with how you set up a test client. From the first glance it looks okay. I did something similar but used a postgres database for testing.

# a single method to create app for both testing and running
def create_app():
   app = Flask(
        __name__,
   )
   app.config.from_object(config_class)
   db.init_app(app) # <- this db is the same which you are using in the main app
   Migrate(app, db)

   # register endpoints
   # app.register_blueprint(some_blp)

   return app


@pytest.fixture(scope="session")
def app():
    test_app = construct_app(app)

    with test_app.test_client() as cl:
        with test_app.app_context():
            db.create_all()
        yield cl
        with test_app.app_context():
            db.session.commit()
            db.drop_all()

This setup should work.

You can check my pet project (repo) which I did in the past where I also wrote tests. It was one of the first projects I had written on flask so there things I would do differently.