Beans (Phaseolus spp.) are one of the most important legumes for their nutritional value and health benefits in many world regions. In addition to Phaseolus vulgaris, there are four additional species that are cultivated in many regions of the world and are a source of food for human consumption: P. lunatus, P. coccineus, P. polyanthus, and P. acutifolius. In this work, phenolic compounds, antioxidant activity, and anti-nutritional compounds of 18 bean accessions, corresponding to four different species of the genus Phaseolus, were analyzed. In addition, their physical characteristics, proximate composition, and amino acid content were determined in order to compare their phytochemical composition and nutritional value. The species closest to each other in terms of essential amino acid content were P. polyanthus with P. vulgaris and P. lunatus with P. coccineus. Furthermore, there was a strong positive correlation between antioxidant activity and flavonoids, anthocyanins, and lectins with all the accessions collected. Significant differences in the content of phenolic compounds were found among the bean species studied. Therefore, in addition to P. vulgaris, other species such as P. coccineus and P. lunatus have high biological and antioxidant potential that could be beneficial to human health when consumed as nutraceutical foods.