Soybeans (Glycine max L.) are a species of legumes which is nutritionally rich source of dietary fibers and phytochemicals such as flavonoids phenolic, and isoflavones. Germination and fermentation is the most effective process to improve the quality of legumes. In this study, Total Phenolic Content (TPC), Flavonoid Content (TFC) and Antioxidant activity of germinated and fermented two different varieties of soybean seed was evaluated. Sprouting of seeds, fermentation, evaluation of TPC, TFC and antioxidant activity of the extract were done by using the standard method as described. The methanolic extracts of black soybean seeds and sprouts have higher antioxidant activity than the yellow soybean seeds and sprouts. Fermentation significantly increased the TPC, TPC and antioxidant activity of soybean seed and sprouts. The highest antioxidant activity was observed in fermented black soybean sprouts extract 88.02% DPPH, 88.54% H2O2, 6.56 eq to ascorbic acid FRAP value and 70.03% of lipid peroxidation inhibition activity. The TPC and TFC were noted 13.18 ± 0.04 mg GAE/gm of extract and 66.9 ± 0.68 mg QE/gm of extract, respectively. A strong positive correlation was observed between phenolic content with antioxidant activity with DPPH (R2=0.8124), H2O2 (R2=0.8092) and FRAP (R2=0.9806), respectively. This study showed that the effect of germination and fermentation enhances Phenolic, flavonoid and antioxidant activity. Thus, germination and fermentation proved to be desirable bioprocess for producing enriched ingredient with health promoting antioxidant compound in a natural way.