Inga edulis Mart. (Fabaceae) is a fast-growing, nitrogen-fixing tree native to Central and South America, being prevalent in the Amazon Basin. It is a versatile and valuable tree species with a wide range of traditional uses and benefits, as well as an important local food. However, despite its wide uses, specific studies focused on understanding the patterns of diversity of I. edulis are still scarce. In this study, we evaluated how morphological and genetic diversity is distributed across natural and planted I. edulis populations, studying a total of 125 samples collected in South Ecuador. Specifically, we asked the following questions: (1) Is genetic erosion occurring in domesticated populations? (2) Does gene flow occur between natural and planted populations? (3) Do different cultivation practices impact the diversity of I. edulis? Our results show that fruits are longer and heavier in planted than in wild trees, contrary to genetic diversity, which was found to be significantly higher in wild trees. Agro-forestry systems where Inga is being used in Cocoa and Coffea plantations showed low diversity. In contrast, trees used by locals in their homes and gardens still maintain high levels of diversity, being a good source for the conservation of raw genetic diversity. Gene flow occurred between natural and wild populations, although different genetic groups were seen in wild trees supporting the presence of genetic erosion in domesticated populations. Understanding and maintaining this genetic diversity is essential for the conservation of genetic resources. This is critical for the long-term sustainability of breeding programs, ensuring that future generations continue to have access to robust and adaptable genetic resources.