Promoting food security is one of the 17 Sustainable Development Goals (SDGs) proposed by the United Nations General Assembly, with a target date of 2030. Human nutrition based on legume consumption is essential to ensuring food security while reducing greenhouse gas emissions associated with nitrogen fertilizer use. Moreover, preserving legume biodiversity is critical to increasing agricultural resilience against climate change. The Andean lupine or “tarwi” (Lupinus mutabilis Sweet) is a legume native to the Andean region with high nutritional importance. Morphological characterization processes allow the determination of local agro-biodiversity and the identification of promising materials for genetic improvement programs. In the present investigation, 173 accessions of Andean lupine from the Germplasm Bank of INIAP, Ecuador, were evaluated. Thirteen quantitative and fifteen qualitative descriptors were used in the characterization. The results revealed that the genetic variability of the Andean lupine is represented by the conformation of four groups of accessions. Among those groups, two accessions stand out for having small plants and high yields, factors that could be used for genetic improvement processes or be reintroduced into farmers’ fields as they represent an option for the production, consumption, and marketing of the local germplasm of this relevant ancient crop. A phenotypic diversity map of the cultivated tarwi explained that areas with high morphological diversity are not completely identical to areas with high ecogeographic diversity. The distribution of the genetic variability of species appears to be more related to cultural aspects than environmental conditions.