AbstractOne of the steps to provide fundamental data for planning a mining effort is the magnetic surveying of a target area, which is typically carried out by conventional aircraft campaigns. However, besides the high cost, fixed‐wing aerial vehicles present shortcomings especially for drape flights on mountainous regions, where steep slopes are often present. Traditional human‐crewed flights have to perform tedious and dangerous trajectories, under strict velocity and attitude constraints. In this paper, we deal with the problem of accomplishing digital magnetic‐elevation maps using autonomous and cooperative aerial robots. The proposed approach for autonomous mapping utilizes a custom‐built fluxgate sensor and off the shelf cameras adapted for small airborne platforms. We also propose an innovative approach for generating a digital magnetic‐elevation model from the gathered data. Our method was evaluated and validated in field tests in an industrial scenario to detect scrap metals in ore piles. Results show that the proposed method could reliably detect magnetic anomalies while generating accurate three‐dimensional magnetic maps.