Low induction number EMI instruments are able to simultaneously measure a soil's apparent magnetic susceptibility and electrical conductivity. This family of dual measurement instruments is highly useful for the analysis of soils and archeological sites. However, the electromagnetic properties of soils are found to vary over considerably different ranges: whereas their electrical conductivity varies from ≤0.1 to ≥100mS/m, their relative magnetic permeability remains within a very small range, between 1.0001 and 1.01 SI. Consequently, although apparent conductivity measurements need to be inverted using non-linear processes, the variations of the apparent magnetic susceptibility can be approximated through the use of linear processes, as in the case of the magnetic prospection technique.Our proposed 3D inversion algorithm starts from apparent susceptibility data sets, acquired using different instruments over a given area. A reference vertical profile is defined by considering the mode of the vertical distributions of both the electrical resistivity and of the magnetic susceptibility. At each point of the mapped area, the reference vertical profile response is subtracted to obtain the apparent susceptibility variation dataset. A 2D horizontal Fourier transform is applied to these variation datasets and to the dipole (impulse) response of each instrument, a (vertical) 1D inversion is performed at each point in the spectral domain, and finally the resulting dataset is inverse transformed to restore the apparent 3D susceptibility variations.It has been shown that when applied to synthetic results, this method is able to correct the apparent deformations of a buried object resulting from the geometry of the instrument, and to restore reliable quantitative susceptibility contrasts. It also allows the thin layer solution, similar to that used in magnetic prospection, to be implemented. When applied to field data it initially delivers a level of contrast comparable to that obtained with a non-linear 3D inversion. Over four different sites, this method is able to produce, following an acceptably short computation time, realistic values for the lateral and vertical variations in susceptibility, which are significantly different to those given by a point-by-point 1D inversion.