Brazilian Atlantic Forest hotspots play an important role in global carbon stock and sequestration. Despite this biome is currently under progressive degradation with direct impacts on soils, little information is available on the dynamics of SOC within aggregates under different land uses in patches of this Atlantic Forest hotspot in Brazilian semi-arid. Three typical land uses (woodland, agroforestry system (AFS), and pasture) and different soil layers (0.0-0.2 and 0.2-0.4 m) were evaluated in the humid highlands of northeastern Brazil. Soil aggregate stability and the OC stock and iron oxides (Fed) in large macroaggregates (LA: > 2 mm), small macroaggregates (SA: 0.25-2 mm), and microaggregates (MA: 0.25-0.053 mm) were evaluated. Land use affects soil aggregation and distribution of size fractions by altering aggregate-associated OC. OC content was significantly higher in large macroaggregates of woodland and the agroforestry system. Large and macroaggregates-associated OC stocks had a dominant effect on aggregate-associated OC stocks in woodland and the agroforestry system, respectively. The OC stock in the bulk soil of AFS is directly related to the proportions and microaggregate-associated OC stock. Iron oxides also strongly influence the formation of large macroaggregates and microaggregates in the agroforestry system. Thus, AFS stabilizes soil carbon in small macroaggregates and microaggregates (associations with soil minerals), constituting an important aspect of carbon cycling in fragile patches of humid Atlantic Forest in Brazilian semi-arid.