The objective of this study was to analyze the biological contribution to macroaggregate formation under cocoa agroforestry systems, as well as to evaluate the potential of macroaggregates to store carbon. The variation of the populations of macrofauna and the relationship with the morphology of aggregates was monitored in five agroforestry systems associated with cocoa established from different land uses, taking as reference the forest and pasture. Some cacao agroforestry systems favored the presence of macrofauna functional groups similar to the forest (p < 0.05). According to the principal component analysis, the effect of land use on macroaggregate formation is highly significant (p < 0.001) and explained 55% of the total variance. The macrofauna and macroaggregates showed significant covariation (RV = 0.22, p-value = 0.001). Biogenic macroaggregates contained more carbon when they came from agroforestry systems.