If everything runs successfully, you should have a new sqlLite database flask_boilerplate_main.db file generated inside the main package. Apply the migration script to the database by using the upgrade command. With sqlalchemy how to dynamically bind to database engine on a per-request basis Flask SQLAlchemy setup dynamic URI I've also seen some examples that were provided for handling sharded databases (which should apply as well, as the databases are essentially sharded logically by client), but, again, nothing specific to Flask-SQLAlchemy.