Magnetometry is one of the most efficient and successful methods of archaeological prospection. Drone-based prospecting is increasingly being used in many fields of remote sensing but with respect to magnetometry, with rather poor results. For magnetic surveys, drone prospecting comes with the problem that magnetic and mechanical disturbances originating from the aircraft decrease the quality of the measurements.Here we present the adaptation of a commercial three-axis fluxgate magnetometer setup, which can be suitable for archaeological prospection, after applying appropriate filter methods and minimising the flying altitude and speed. For approval of the system, we performed drone-based surveys in high spatial resolution (50 cm line spacing) at constant, ultra-low sensor altitudes of 45 ± 10 cm and 75 ± 10 cm. We chose an archaeological site from the roman period as survey site (3.8 ha), where high-quality ground-based caesium magnetometer data was available. This allows us to demonstrate the first detailed comparison of drone-based and ground-based magnetic survey data for archaeology. For further evaluation, the influence of the drone on the measurements is assessed, drift and sensor resolution checks are carried out, and suitable data filtering methods are evaluated.Our results show that we can detect main archaeological features such as ditches, pits, fireplaces and remnants of stone fundaments with the drone-based setup, which are the relevant structures for the majority of archaeological prospections worldwide. Further, we can prove that the data quality can significantly be increased by lowering the flight altitude and speed. We conclude that drone-based magnetometry serves above all to cover large and inaccessible areas in short time. Our findings are a first step towards the development of standards for drone-based archaeological prospection approaches.