Promoting diverse and functioning biological communities is an important objective of agroecology, with increasing attention given to the important role of soil biodiversity. In an experimental study conducted under field conditions, we followed over four years the dynamic of soil organisms from various sizes and trophic niches in four variants of a cropping system which are differentiated by soil tillage, residue management and N fertilization rate. Differentiation in overall family diversity, as well as in the abundance and diversity of the multiple trophic groups was evaluated every two years. Our study demonstrated a delayed but effective differentiation in soil biota diversity following implementation of the agricultural practices. Soil biodiversity varied throughout time with some groups responding more readily than others, thereby highlighting differences related to trophic position and body size. The visualization of diversity profiles revealed an increasing impact of agricultural practices on group diversity towards higher trophic levels. While tillage appeared a main factor of influence, surprisingly little impact of residue management and nitrogen fertilization could be observed. Predicting the response of the soil biota to anthropogenic influence calls for an understanding of complex interactions between soil organisms in heterogeneous soil microhabitats. Through its multitaxonomic approach, the present study increases our understanding of the dynamic of soil communities in agricultural cropping systems and helps identify possible consequences for soil functioning.