BACKGROUND: Traditional soy-fermented foods, such as miso, douche, natto, and tempeh have been widely used as a dietary supplement in Asian countries, and numerous reports on their phenolics and antioxidant activities have been published. Soy germ contains 10-fold higher phenolics than whole soybean, hence using soy germ as fermentation substrate will be more efficient than whole soybean. RESULTS: Soy germ fermented with Aspergillus niger M46 resulted in a high-efficiency bio-transformation of phenolics and flavonoids to their metabolites, and a diverse secondary metabolic product was also found to response oxidation stress of fungal colonisation. Its antioxidant activity against hydroxyl radicals and superoxide radicals (IC50 = 0.8 and 6.15μg mL-1, respectively) was about 205-fold and 47-fold higher than those of unfermented soy germ (IC50 = 164.0 and 290.48μg mL-1), respectively. These results were similar to those observed for Trolox, and more active than those of BHT and hesperidin. The β-glucosidase and α-amylase produced during fermentation were mainly responsible for mobilisation of the phenolics. CONCLUSION: Our results demonstrate that fermented soy germ has the potential to be a good dietary supplement for prevention of oxidative stress-related diseases, and the solid-state bioprocessing strategy could be an innovative approach to enhance the antioxidant activity of soy germ.