The aim of this study was to evaluate the stock of total organic carbon (TOC) and to perform the physical-granulometric fractionation of soil organic matter (SOM) in different management systems (MS). Three MS and one reference area of Native Forest (NF) were studied, and the three systems were sugarcane (SC), permanent pasture (PP) and no-tillage system (NTS). Soil samples were collected in the 0–0.05, 0.05–0.10, 0.10–0.20-m layers. Soil density (Sd), TOC, stratification index (SI), carbon stock (StockC), variation in StockC (∆StockC), carbon content of particulate organic matter (C-POM) and mineral organic matter (C-MOM), carbon stock index (CSI), lability (L), lability index (LI), and carbon management index (CMI) were determined. The MS presented higher Sd than the NF area. The NF area had higher TOC contents in the first layers, reaching 25.40 g kg-1 in the 0–0.05-m layer, with the PP area having higher values than the NF in the 0.10–0.20-m layer. The NF area showed the highest levels of C-POM (15.25 g kg-1) and C-MOM (10.15 g kg-1) in the first layer. In the 0.10–0.20-m layer, the PP and NTS systems were superior to the others. Regarding the C-MOM content, SC and PP showed higher levels in the 0.10–0.20-m layer. The highest CMI values were observed in the NTS and PP areas in the 0.10–0.20-m layer. The MS increased the Sd and reduced the TOC levels. The different MS modified the POM fraction, and the MOM fraction was most impacted by the SC area. The lability of the SOM was altered by the MS in the most superficial layers.