Common beans (Phaseolus vulgaris), comba beans (Phaseolus lunatus), and ayocote beans (Phaseolus coccineus) are the most consumed beans worldwide. This work aimed to analyze the nutraceutical potential, antinutritional content, antioxidant activity, and physicochemical characteristics of 38 native bean accessions from South Pacific Mexico. Regarding size, the accessions collected from P. lunatus were the longest (15.31 ± 1.31 mm) and widest (11.04 ± 0.85 mm), while those of P. coccineus were of a greater thickness (6.40 ± 0.85 mm). In addition, it was observed that P. vulgaris species presented a higher percentage of protein and fat content. Moreover, an inverse correlation was found between the content of carbohydrates, fats, and proteins in all the collected accessions. The main free amino acid of P. lunatus and P. vulgaris was tryptophan with concentrations of 35.36 ± 0.37 mg/100 g and 47.41 ± 0.53 mg/100 g, respectively. While P. coccineus contained isoleucine as its main free amino acid with a concentration of 29.85 ± 1.06 mg/100 g Furthermore, the collected accessions could be 100% correctly classified as P. vulgaris, P. lunatus, or P. coccineus according to the free amino acid content; this classification could serve as a marker to distinguish between Phaseolus species. In addition, principal component analysis of the phenolic compound content, nutritional composition, antinutritional factors, and antioxidant activity was performed, showing not only that P. vulgaris accessions can present nutraceutical potential but also that some accessions from P. lunatus and P. coccineus species can be promoted for the development of functional foods.