Optimal use of resources in agroforestry requires the evaluation of multi-species and multi-strata cropping systems. The current study evaluated the effect of plant diversity on the performance of agroforestry systems in Talamanca, Costa Rica. Plants in nine 100-m2 plots in each of 20 fields were classified into five groups (banana, cacao, other fruits, timber, and firewood), and diversity was assessed by the Shannon–Wiener index. The production of each individual plant was estimated and converted into income according to local market prices. Our results indicated that as plant diversity increased, the income derived per plant increased for other fruits, firewood, and timber and also when all cultivated plants were considered as one group. In contrast, the income derived per plant decreased for banana and cacao as diversity increased. This suggests that complementarity between plants was stronger than competition for those plants occupying the higher strata of the canopy (i.e., other fruits, firewood, and timber) but that competition was stronger than complementarity for plants occupying the lower strata of the canopy (i.e., banana and cacao). These results increase our understanding of how the composition and the organisation of these agroforestry systems may be optimized.