Six two-year cropping sequences which varied in CI were evaluated (Fig. 1). They were: i) soybean monoculture (S-S), ii) soybean with a previous wheat cover crop (CC) (CC/S-CC/S), iii) wheat/soybean sequential double crop, i.e. two crops in the same year (W/S-W/S), iv) two sole crop rotation with soybean followed by maize (S-M), v) soybean with maize rotation including a previous wheat CC before soybean (CC/S-M) and vi) three-crop wheat/soybean-maize (W/S-M) rotation. Treatments were established in a randomized complete block design with four replicates. Plots were 5 m wide and 30 m long. Both experimental sites had similar slopes (5.2%) and terraces for erosion control. Our work is focused on the initial effects (two year after the beginning of the experiment) of CI on total sequence yield, crop residue input, SOC stocks and soil aggregation. This is a critical period that strongly influences farmer’s adoption of management strategies, such as crop rotation or the use of cover crops. However, the adoption of a new management strategy for the farmers is often more based on crop yield than on soil variables. Therefore, the improvement in soil health indices by the adoption of sequences with a higher CI should be reached maintaining or even increasing total crop yields.