In this study, four common beans (Phaseolus vulgaris L.), navy, black, pinto, and small red beans were processed to common bean natto. Four types of common beans fermented with Bacillus subtilis natto were investigated for phenolic composition and antioxidant activity. There was a significant increase in TPC in navy beans and pinto beans after fermentation with B. subtilis natto (p < 0.05). Prolonged fermentation of up to three days did not increase the FRAP and DPPH values of common beans compared to cooked beans. However, ORAC values for black beans and pinto beans started to increase after fermentation for two days, and all four common beans showed increased ORAC values after 3 days of fermentation. The phenolic acid profiles of these common beans were altered after fermentation with B. subtilis natto, such as certain phenolic acids and anthocyanins have either increased or decreased, ex. Caffeic acid derivative of navy beans increased significantly from 68.99 μg/g bean to 83.91 μg/g bean after 3-days fermentation. These findings demonstrate that fermented common beans have higher phenolic content and antioxidant activities, potentially developing into novel bean-based products and promoting health.