Application of microbial stress to soybean during germination induces the accumulation of phytoalexins, which have many health benefits. In this study, the effects of stress induced by Aspergillus oryzae on the phytochemical composition of germinating soybeans were investigated, and their radical scavenging activity was compared with those of ungerminated (US) and germinated (GS) soybeans. Additionally, the antioxidant activity of coumestrol, a soybean phytoalexin, against hydrogen peroxide-induced reactive oxygen species (ROS) was investigated in HepG2 cells. A. oryzae exposure significantly decreased the total isoflavone content and induced coumestrol and glyceollin I. A. oryzae-challenged germinated soybeans exhibited the highest radical scavenging activity (IC(50) = 0.55 mg/mL) as compared to US and GS. Coumestrol exhibited significantly higher radical scavenging activity than daidzein and genistein. Furthermore, coumestrol significantly prevented hydrogen peroxide-induced ROS production and lipid peroxidation and inhibited decreases in cell viability, intracellular glutathione (GSH) levels, and superoxide dismutase (SOD) activity. These results indicate that using food-grade A. oryzae to elicit the biosynthesis of phytoalexins alters the secondary metabolite profiles of the soybeans and offers enhanced bioactivity of soybean as a functional food ingredient.