Abstract Marine magnetometry very close to the targeted sources, even in very deep waters, is today a reality with the advent of autonomous underwater vehicles. We argue that a successful approach is to fully integrate the magnetometer onboard the autonomous underwater vehicle and to deal with its static magnetic noise, that is induced and permanent fields of the drone, with a 3‐axis vector measurement of the Earth's magnetic field. This argument is supported by results from three magnetic surveys performed with different fluxgate magnetic sensors embedded in autonomous underwater vehicles of increasing sizes. They show that simple specifically defined figures of merit coupled to an optimized scalar calibration procedure derived from aeromagnetic and satellite‐borne developments produce reliable magnetic measurements from autonomous underwater vehicles for geophysical mapping or detection applications. Results are impressive and show that even weak magnetic anomalies smaller than 10 nT can be highlighted even though the magnetic signatures of autonomous underwater vehicles can be orders of magnitude higher.