Fluxgate 3-axis magnetometers are seldom used on archaeological sites due to their lack of precision. Nonetheless, they offer light weight, low power consumption and the ability of compensation of the magnetization of the prospecting device. This study proposes to use calibration and compensation processes developed for space research and aerial measurement to build a multi-sensor and georeferenced device to assess deep and shallow objects for large-scale archaeological investigations in Qasr 'Allam, in a context of heavy sedimentary coverage and uneven surface. The use of the device on the site in combination with potential field transformations of the signal such as the double reduction to the pole and the vertical derivative reveal a vast irrigation system as well as a large religious facility. A comparison with gradiometric measurements shows a resolution as good at least for shallow sources. The precise positioning allows targeted excavations that validate the geophysical interpretations and offer new archaeological information. These discoveries give enough proof to the local authorities to define the area to be protected from the threatening progression of agricultural fields.