How to make Flask-SQLAlchemy automatically rollback the session if an exception is raised?

you can do something like this:

@app.teardown_request
def teardown_request(exception):
    if exception:
        db.session.rollback()
    db.session.remove()

Have a look here for teardown_request info. You might need to set the PRESERVE_CONTEXT_ON_EXCEPTION config variable if you are in debug mode.