During the past few decades, commercial silvopastoral systems (SPS) with exotic Eucalyptus (hybrid) trees have become popular in the Brazilian Cerrado (savanna). With the increasing awareness about the role of carbon (C) storage in soils as a climate-change mitigation strategy and the relationship between the nature of soil aggregates and the soil's carbon sequestration potential, it is important to understand the influence of such SPS systems on soil organic carbon (SOC) storage. We studied C content in three aggregate size classes in six land-use systems on Oxisols in Minas Gerais, Brazil. The systems were planted forest, native secondary forest, managed pasture, and three 8-year-old SPS, differing in their tree-planting configurations. Eucalyptus hybrid was the tree in SPS and planted forest treatments, and Urochloa decumbens was the grass in SPS and pasture treatments. From each treatment, replicated soil samples were collected from four depth-classes (0–10, 10–30, 30–60, and 60–100 cm), fractionated by wet sieving into the three aggregate-size classes, 2000 to 250 μm, 250 to 53 μm, and <53 μm size classes representing macroaggregates, microaggregates, and silt + clay, respectively, and their C contents determined. Down to 1 m, total SOC stock values ranged from 260 Mg ha−1 under pasture to 167 Mg ha−1 under native forest, with 174 Mg ha−1 for Eucalyptus plantation and about 195 Mg ha−1 for the three SPS. Compared to the degraded native forest, the pasture system had significantly higher SOC in the whole soil and the aggregate size fractions, especially in the lower soil-depth classes. The lower SOC stock of Eucalyptus hybrid SPS compared to open pasture differs from the general trend of SPS having higher stock. Given that the Cerrado biome is a biodiversity hotspot, the use of native nitrogen-fixing trees, of which there are several, is worth investigating. In addition, the conversion from Eucalyptus monocultures to SPS could be considered as a strategy to increase the SOC stock.