In the agropastoral system (pasture–soybean [PS] rotation system) initiated in 1993 in Brazilian savannas (Cerrados) in Campo Grande, Mato Grosso do Sul State, Brazil, the changes in soil carbon (C) and nitrogen (N) and the natural carbon stable isotope (¹³C) signatures to determine the origin of soil C were examined. In this study, three primary cultivation systems were tested: 1) continuous pasture (P) (Brachiaria decumbens), 2) continuous soybean (S), and 3) PS rotation (4 years of soybean cultivation after 4 years of pasture). Mineralized N levels decreased after introducing soybean in the S and PS rotation fields. Using the ¹³C natural abundance technique, 27% and 13% of soil organic C was estimated to be derived from soybean residues in the S and PS after the 8-year experiment, respectively. Thus, soybean cultivation replaced soil C by C derived from soybean residues to some extent and stimulated the degradation of soil organic matter due to the return of soybean residues with low C/N ratio and tillage system. Furthermore, larger negative N balances in the S and PS were estimated compared with the P cultivation system.