Geomagnetic prospection is an efficient and environmentally friendly geophysical method for the analysis of the magnetic minerals’ distribution in the subsurface. High-resolution measurements require on-ground campaigns. However, these activities might imply high costs, risk and time consumption. Some more recent works have started to use magnetometers on-board remote piloted aircrafts. Normally, they fly at a constant altitude and use scalar probes. This configuration permits the determination of the magnitude of the magnetic field but not the direction, and requires advanced techniques for in-depth interpretation of the sources. In this manuscript, we describe the accommodation of a system for vector magnetometry in a drone whose flight altitude follows the elevation of the terrain. This singularity improves the capability of interpretation, including constraints in dating due to the record of the geomagnetic field. The work consists of the design, development and implementation of a solidary payload system anchored to the body of the platform in order to determine the vector magnetic field. It describes the details of the system and the performance characteristics obtained after the calibration, as well as its demonstration via a field campaign in the spatter deposits of Cerro Gordo volcano in Campos de Calatrava volcanic province in Spain.