Enhancement of organic matter plays an essential role in improving soil quality for supporting sustainable food production. Changes in carbon stocks with impacts on emissions of greenhouse gases may result from the stratification of organic matter as a result of soil use. The objective of this study was to evaluate the impact of soil management systems on soil carbon stocks and stratification ratios (SR) of soil organic matter pools. Total organic carbon (TOC), particulate organic carbon (POC), mineral-associated organic carbon, microbial biomass carbon (MBC) and nitrogen, basal respiration, and particulate organic matter nitrogen (PON) were determined. The field experiment comprised several tillage treatments: conventional tillage, no-till with biannual rotation, no-till with biannual rotation combined with a second crop, no-till with annual rotation, and pasture. The labile fractions indicated a high level of variation among management systems. Pasture proved to be an excellent option for the improvement of soil carbon. While the conventional tillage system reduced total carbon stocks of the soil (0-40 cm), no-tillage presented TOC stocks similar to that of native vegetation. Sensitivity of the TOC SR varied from 0.93 to 1.28, a range of 0.35; the range for POC was 1.76 and for MBC 1.64. The results support the hypothesis that the labile fractions (POC, MBC, and PON) are highly sensitive to the dynamics of organic matter in highly weathered soils of tropical regions influenced by different management systems. Reductions to SRs of labile organic matter pools are related to the impacts of agricultural use of Cerrado soils.