The objectives of this study were to evaluate the stability of aggregates, and quantify the contents and stocks of total organic carbon (TOC), and granulometric and humic fractions of soil organic matter (SOM). Four management systems were evaluated: (1) a no-tillage system (NTS) implemented 5 years ago (NTS5); (2) NTS implemented 17 years ago (NTS17); (3) conventional tillage system (CTS) implemented 20 years ago (CTS20); and (4) native Cerrado vegetation. For each system, five undeformed and five deformed soil samples were collected from the 0.00–0.05, 0.05–0.10, 0.10–0.20, and 0.20–0.40 m layers. The weighted mean diameter (WMD), TOC, stock of carbon (StockC), organic carbon particulate (OCp), organic carbon associated with minerals (OCam), stock of OCp, stock of OCam, carbon stock index, carbon management index (CMI), organic carbon in the fulvic acid fraction (FAF), humic acid fraction (HAF), and humin fraction were quantified. The WMD and CMI values increased as the soil management intensity decreased. The adoption of the NTS increased the WMD and the contents, stocks, and proportions of TOC in the more labile granulometric and humic (FAF/HAF) fractions of the SOM. The WMD, CMI, granulometric and chemical fractionation of the SOM were more efficient than the TOC and StockC in identifying the differences between the management systems. Due to the higher contents of the more labile fractions of SOM, the granulometric and chemical fractionation of SOM in the NTS5 and NTS17 systems had higher values of WMD and CMI than the CTS20 system.