Understanding carbon (C) and nitrogen (N) sequestration in diversified cropping systems provides a pivotal insight for soil health management. Here, the soil was sampled from an ongoing field experiment (five years) with three cropping systems: i) winter wheat/summer maize, ii) winter wheat/summer maize-early soybean, and iii) fallow. We evaluated C and N stocks in aggregates for topsoil (0–20 cm) and subsoil (20–40 cm) depending on cropping systems by comparison of three aggregate fractionation methods (dry, optimal-moisture, and wet sieving). Although the fertilizer application rate for wheat/maize was twice as much as for wheat/maize-soybean, this resulted in similar C and N stocks in the topsoil. The N stock, however, was 13% higher under wheat/maize-soybean than under wheat/maize in the subsoil due to N2 fixation by soybean. The C and N stocks decreased by 22% and 12% under fallow compared to wheat/maize in the topsoil. The wheat/maize-soybean cropping system increased soil aggregates size when estimated by dry and optimal-moisture fractionations. The aggregate size distribution shifted from the dominance of large (> 2 mm) toward small macroaggregates (0.25–2 mm) with increasing moisture used by fractionation due to the low stability of large macroaggregates. Thus, the combination of dry and optimal-moisture sieving is the preferred method to characterize aggregate stability. Overall, diversified cropping systems increase soil aggregation and stability, thus have great potential to enhance soil C and N stocks. © 2022 Elsevier B.V.