Diverse agroforestry systems conciliate food production, biodiversity conservation, and the provision of ecosystem services as atmospheric carbon sequestration. However, the role of floristic richness in the production of biomass in these systems is not clear. This study evaluated the effect of species richness and vegetation structure on aboveground biomass carbon in different agroforestry systems in the Southern Amazon of Bolivia. For that, 25 agroforestry systems and 4 secondary forests were studied in the departments of Santa Cruz and Beni. In each system, a 1 963 m2 circular plot was installed, where the vegetation (trees, shrubs and herbaceous) and necromass (leaf litter, branches and dead trees) were sampled. Linear and logarithmic functions were used to evaluate the effect of vegetation richness and structure on carbon, and the variance partition was used to examine the pure and shared effect of the richness and vegetation structure variables on carbon. Regressions showed a positive strong relationship between species richness and carbon (r2 = 0.74; P < 0.001). The partition of carbon variance showed that richness, structure and variation of the structure explained 85.7 %. Alone the richness explained 12.7 %, the structure 8.8 % and the variation of the structure 4.8 %. These results confirm that carbon in the aboveground biomass increases with species richness and structural variation of the vegetation. Therefore, more biodiverse and stratified agroforestry systems are more efficient in the use of resources and can contribute with climate change mitigation.