Purpose The mineralization/immobilization of nutrients from the crop residues is correlated with the quality of the plant material and carbon compartments in the recalcitrant and labile soil fractions. The objective of this study was to correlate the quality and quantity of crop residues incubated in the soil with carbon compartments and CO 2 -C emission, using multivariate analysis. Materials and methods The experiment was conducted in factorial 4 + 2 + 5 with three replicates, referring to three types of residues (control, sugarcane, Brachiaria, and soybean), and two contributions of the crop residues in constant rate, CR (10 Mg ha −1 residue), and agronomic rate, AR (20, 8, and 5 Mg ha −1 residue, respectively, for sugarcane, soybean, and Brachiaria), evaluated five times (1, 3, 6, 12, and 48 days after incubation). At each time, we determined the CO 2 -C emission, nitrogen and organic carbon in the soil, and the residues. In addition, the microbial biomass and water-soluble, labile, and humic substance carbons fractionated into fulvic acids, humic acids and humin were quantified.Results and discussion Higher CO 2 -C emissions occurred in the soil with added residue ranging from 0.5 to 1.1 g CO 2 -C m −2 h −1 in the first 6 days of incubation, and there was a positive correlation with the less labile organic soil fractions as well as residue type. In the final period, after 12 days of soil incubation, there was a higher relation of CO 2 -C emission with carbon humin. The sugarcane and soybean residue (20 Mg ha −1 ) promoted higher CO 2 -C emission and the reduction of carbon residue. The addition of residue contributed to an 82.32 % increase in the emission of CO 2 -C, being more significant in the residue with higher nitrogen availability. Conclusions This study shows that the quality and quantity of residue added to soil affects the carbon sequestration and CO 2 -C emission. In the first 6 days of incubation, there was a higher CO 2 -C emission ratio which correlates with the less stable soil carbon compartments as well as residue. In the final period of incubation, there is no effect of quality and quantity of residue added to soil on the CO 2 -C emission.