Integrated production systems composed of trees, crops and pastures have shown good results in improving soil quality and the capacity to store carbon in the soil, being efficient in mitigating greenhouse gas emissions. Despite this, changes in carbon stocks and soil organic matter fractions in the initial stages of implementing an agroforestry system remain unclear. This study evaluated the carbon balance and the dynamics of soil organic matter fractions in an agroforestry system conducted over a decade. Total carbon, labile carbon, carbon from particulate organic matter, organic carbon associated with minerals and inert carbon were determined at depths 0–10 cm, 10–20 cm and 20–40 cm. Soil carbon stocks were also estimated for the 0–40 cm depth. Total carbon increased in the agroforestry system compared with a low-productivity pasture. The total carbon stock in the last growing season (68.57 Mg ha−1) was close to the original soil stocks under native Cerrado vegetation (76.5 Mg ha−1). After 10 years, there was a positive balance in the soil carbon stock of both the total carbon and the soil organic matter fractions. The successional agroforestry system is a good alternative to increasing soil total carbon stocks and labile and non-labile fractions of soil organic matter.