Agroforestry is increasingly framed as a nature-based climate change mitigation strategy, but the relationship between biodiversity and carbon storage across structurally and management-divergent systems remains unclear. This study compares carbon stocks and biodiversity of six agroforestry systems representing four typologies in Thailand, with an emphasis on the degree to which stand structure plays a role. Carbon stocks were predicted from above-ground biomass, below-ground biomass, and soil organic carbon—while biodiversity was described by species richness, Shannon diversity, and evenness. Structurally defined properties were used to determine how spatial patterns of biomass affect biodiversity–carbon relationships. Carbon stocks varied significantly across systems. Rubber monoculture systems, known for strong dominance of one plant, contained the most biomass carbon; however, more diverse systems stored less overall. When all the systems were examined in an integrated way, greater diversity meant lower carbon. However, that relationship weakened when dominance-driven systems were removed and evenness had a positive association with carbon storage. These findings suggest that the detected biodiversity–carbon relationship is highly dependent on stand structure. Instead of being a universal trade-off, the relationship depends on how biomass is partitioned among species. This illustrates the influence of structural attributes in ecosystem functioning and indicates how agroforestry systems may be configured to improve carbon storage with regard to biodiversity goals.