Inga edulis Mart. (Fabaceae) is a culturally and economically important fruit tree in Ecuador, valued for its fast growth, nitrogen-fixing capacity, and large, edible pods. Despite its widespread use in traditional agroforestry systems, little is known about how cultivation practices influence its morphological and genetic diversity. In this study, we assessed fruit traits of and genetic variation in I. edulis across natural, agroforestry, and home garden populations in southern Ecuador. Trees cultivated in agroforestry systems produced significantly longer (mean = 79.3 cm) and heavier pods (mean = 0.62 g), reflecting a focus on fruit yield. However, these populations exhibited reduced genetic diversity (for instance, the mean number of alleles = 10.1). In contrast, home garden trees retained higher levels of genetic variation (the mean number of alleles = 15.2), despite producing shorter (mean = 39.3 cm) and smaller fruits (mean = 0.51 g). These findings highlight a trade-off between productivity and genetic diversity: while agroforestry promotes pod yield, home gardens function as reservoirs of intraspecific variation. Integrating both systems can enhance sustainable management, conservation, and breeding strategies, ensuring the resilience of crops under changing socio-environmental conditions.