Cacao agroforestry systems (AFSs) have high potential for carbon (C) accumulation in weathered soils, but the chemical characterization of C compounds remains poorly understood. This information is key to understanding soil organic matter (SOM) dynamics. Thus, the chemical composition of organic matter within density fractions was determined in different cacao AFS in Brazil. The land-use systems studied were three older cacao AFS (cacao "cabruca," cacao + erythrina, and cacao + rubber tree) and two younger cacao + rubber tree AFS (one replacing a pasture and another replacing a natural forest), which were compared with natural forest and pasture. Physicochemical fractionation (POMc = coarse intra-particulate organic matter, POMf = fine intra-particulate organic matter, and C-m = soil organic carbon associated with the mineral fraction) was combined with diffuse reflectance infrared Fourier transform spectroscopy on soil samples at 0-10 and 80-100 cm. There was generally a reduction in the organic C content of macroaggregate density fractions in the topsoil of younger cacao AFS. On the other hand, the mass and organic C content of microaggregate density fractions at both depths and of macro-aggregates at 80-100 cm were not influenced by soil disturbance. The mass distribution and C content of density fractions showed dissimilarities between the reference sites (natural forest and pasture) and the older cacao AFS. The rA% results revealed dissimilarities between natural forest, pasture, and older cacao AFS from younger cacao AFS. Land use systems can alter the functional groups and stability of SOM fractions. The chemical composition reflected soil disturbance in the cacao AFS implantation. The C-m fraction was the major compartment of soil organic carbon with a significant presence of labile compounds, mainly in the 0-10-cm depth. The effect of land use systems should not only be assessed in terms of total C stocks, but also with respect to changes in C chemical composition, stability, and function.