Production systems that promote the accumulation of soil organic matter (SOM) must be implemented to maintain the sustainability of agriculture, livestock, and forestry. Since increases in MOS content contribute to improving the chemical, physical, and biological quality of the soil, as well as helping to reduce carbon emissions to mitigate climate change. Therefore, the objective of this study was to evaluate soil organic carbon (SOC) and nitrogen (N) stocks after the implementation of agrosilvopastoral (ASP) systems in a Cerrado-Caatinga transition zone in Brazil. Native vegetation of Cerrado-Caatinga (NV), regenerating stratum of Cerrado-Caatinga (RS), two arrangements of ASP systems cultivating Cenchrus ciliaris L. intercropped with Eucalyptus camaldulensis Dehnh. × Eucalyptus tereticornis Sm. hybrid (ASP1 and ASP2), and intercropped with Eucalyptus urophylla S.T. Blake × Eucalyptus grandis W. Mill ex Maiden hybrid (ASP3 and ASP4) were evaluated. Soil C and N stocks and the C content in the humic fractions of SOM were evaluated at 0–10, 10–20, and 20–30 cm soil depths. The introduction of ASP2, ASP3, and ASP4 systems in an area previously occupied by low productivity pasture increased and restored SOC stocks to levels found in NV, at a depth of 0–30 cm. N stocks were higher in ASP systems, regardless of the arrangement studied. As a result, the ASP systems provided accumulations that ranged from 1.0 to 4.31 Mg SOC ha−1 yr−1 and from 0.33 to 0.36 Mg N ha−1 yr−1. The carbon contents in humic fractions remained higher in NV. The hierarchical grouping and principal component analysis showed that the implementation of the ASP systems was efficient in increasing soil C and N stocks over time. In conclusion, the present study identified that integrated production systems can support land use intensification strategies based on sustainable and low-carbon agriculture in a transition area between the Cerrado and Caatinga biomes in Brazil.