This work aimed to obtain and characterize anthocyanin-rich extracts (ARE) from native black beans and evaluate their antioxidant and anti-inflammatory potential. The initial extract was obtained by supercritical fluids (RE) and purified using Amberlite®XAD-7 resin (PE). RE and PE were fractionated using countercurrent chromatography, and four fractions were obtained (REF1 and REF2 from RE, PEF1, and PEF2 from PE). ARE and fractions were characterized, and the biological potential was evaluated. ABTS IC50values ranged from 7.9 to 139.2 (mg C3GE/L), DPPH IC50ranged from 9.2 to 117.2 (mg C3GE/L), and NO IC50ranged from 0.6 to143.8 (mg C3GE/L) (p< 0.05). COX-1 IC50ranged from 0.1 to 0.9 (mg C3GE/L), COX-2 IC50ranged from 0.01 to 0.7 (mg C3GE/L), and iNOS IC50ranged from 0.9 to 5.6 (mg C3GE/L) (p< 0.05). The theoretical binding energy for phenolic compounds ranged from −8.45 to −1.4 kcal/mol for COX-1, from −8.5 to −1.8 kcal/mol for COX-2, and from −7.2 to −1.6 kcal/mol for iNOS. RE and REF2 presented the highest antioxidant and anti-inflammatory potential. Countercurrent chromatography effectively isolates and purifies bioactive compounds while maintaining their biological potential. Native black beans present an attractive phytochemical profile and could be used as ingredients in nutraceuticals and functional foods.