A bacterial strain, initially identified as B1-3, was isolated from cheonggukjang, a traditional Korean dish made from fermented soybeans. Using the Biolog system and 16S rRNA sequence analysis, we identified B1-3 as Bacillus mojavensis. We manufactured a quickly fermented soybean (QFS) food product using the B. mojavensis, and guided by their 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging ability. We isolated substances with antioxidative activity from it. Using mass spectrometry (MS) and nuclear magnetic resonance (NMR) techniques, we isolated 4 compounds from the ethyl acetate (EtOAc)-soluble neutral fraction of methyl alcohol (MeOH) extracts of the QFS food product (genistein, daidzein, 3R,4R-3-methyl-3,4-dihydroxy-2-pentanone, and 3S,4R-3-methyl-3,4-dihydroxy-2-pentanone) and 3 compounds from its acidic fraction (4-hydroxyphenylacetic acid, genistin, and daidzein). Two compounds from the neutral fraction (3R,4R-3-methyl-3,4-dihydroxy-2-pentanone and 3S,4R-3-methyl-3,4-dihydroxy-2-pentanone) were not detected in nonfermented soybeans (NFS) or in the filtrate of the LB broth used to culture B. mojavensis. However, they were detected in the filtrate of the same broth when it contained 2% glucose. These results suggest that these 2 compounds were derived from glucose (or other saccharides) in the soybean during fermentation. One compound that was found in the acidic fraction (4-hydroxyphenylacetic acid) was readily detected in NFS, but not in the culture broth. This suggests that 4-hydroxyphenylacetic acid was derived from NFS. We concluded that the antioxidative activity of cheonggukjang is a result of the interactions between soybean components and the microorganisms used in the fermentation of cheonggukjang.