Agroforestry systems allow conservation of natural resources and promotion of sustainable agriculture in the Ecuadorian Amazon. Nevertheless, the benefit of the associated species that are part of these production systems needs to be demonstrated. The aim of this study was to find out the influence on the crop yield, carbon sequestration, presence of earthworms, and the nutritional contribution of legume species associated with the naranjilla (Solanum quitoense) crop in an agroforestry system. The research was carried out in the Palora Experimental Farm of INIAP, using a randomized complete block design with three replications. The treatments were made up of cultivation systems (agroforestry systems with or without 50% fertilization) and monoculture as a control, with two levels of conventional fertilization (50 and 100%). In the agroforestry arrangements, Gliricidia sepium and Flemingia macrophylla were used to supply biomass. The results showed that during the three evaluation cycles, the yield of naranjilla was influenced by the quality of the biomass added to the soil and not by the amount of synthetic chemical fertilizer that was supplied. The biomass of G. sepium and F. macrophylla provided a greater amount of Mg, Mn, Zn, B, and Fe; elements that contributed to crop yield and the presence of earthworms. The results suggest that the use of legume species in agroforestry systems positively influenced naranjillla productivity, favoring sustainable agriculture in the Ecuadorian Amazon.