A methodology was developed in order to estimate wind erosion by comparing the differences in soil loss with a 3D laser scanner inside a wind tunnel, to relate the change in soil micro-relief to soil loss. We evaluated the effectiveness of a low-cost laser scanner in a wind tunnel for examining the wind-dependent variation in soil surface micro-topography, thereby enabling soil wind erosion to be quantified both quickly and accurately. We, therefore, studied the effect of soil crusting in an intensive horticultural crop, low-tilled soil (once a year) in cereal cultivation, and tilled soil (several times a year) in an ecological citrus orchard, paying attention to the changes occurring when soils are tilled. Moreover, we observed an aggregation effect of CaCO₃ in the wind-erodible fraction, a protective effect of surface stoniness against a direct impact of wind and the incidence of soil particle content. Different behaviour, in terms of random roughness, is due to more stones and/or remnant vegetation being highly resistant to wind in Calcisol, Cambisol, Fluvisol and Arenosol plots, thus increasing surface roughness. In Anthrosol and Leptosol plots, on the contrary, initial roughness was due to large unstable and wind-eroded aggregates which resulted in a decreased surface roughness.