Lupinus is recognized as a nutrient-dense legume rich in protein, raw fiber, antioxidants, and unsaturated fatty acids, contributing significantly to human nutrition and health. In Ecuador, the Andean Crops and Plant Genetic Resources program of INIAP maintains a germplasm bank comprising 257 uncharacterized accessions. This study aimed to evaluate the nutritional and phytochemical composition of ten promising sweet Lupin genotypes (L. mutabilis) exhibiting good agronomic characteristics, resistance and/or tolerance to biotic and abiotic stresses, superior grain quality and significantly reduced seed alkaloid content in experimental trails. These genotypes were compared with two accessions of L. albus and L. angustifolius used as control genotypes. Except for carbohydrate content, L. mutabilis genotypes exhibited similar or superior nutritional profiles compared to genotype controls with high protein (44.7%), fat (19.91%), and ash (4.16%) contents and reduced alkaloid concentrations, notably, two genotypes LmAnds16 and LmFRs43 with 0.04%. However, it exhibited the highest polyphenol (8.84 mg·g⁻¹) and flavonoid (0.67 mg·g⁻¹) concentrations and antioxidant activity for ABTS (19.94 µmol TE·g⁻¹) and FRAP (300.30 µmol TE·g⁻¹) on a dry weight basis (DW). These results are important for the generation of new varieties of Lupinus focused on its nutritional quality and to produce nutraceutical and functional foods.