Isoflavone distribution and ${eta}$-glucosidase activity in cheonggukjang, a traditional Korean whole soybean-fermented food prepared with or without addition of Bacillus subtilis, were analyzed every 6 hr for 36 hr. Thermal cooking of raw-soaked soybeans significantly increased ${eta}$-glucoside isoflavone level by 57.1 % and decreased malonyl-${eta}$-glucosides by 57.6% (p<0.05). Consistent changes of isoflavone profiles in cheonggukjang without B. subtilis addition (COB) and samples with addition of B. subtilis (CWB) were not observed during 36 hr fermentation. ${eta}$-Glucosides of isoflavones are major forms in both COB and CWB. ${eta}$-Glucosidase activity in cheonggukjang decreased significantly compared to that of soaked soybeans due to thermal denaturation, while recovery of enzyme activity in COB was observed. Two new unidentified peaks were detected, and their relative peak areas in CWB were significantly larger than those in COB with increasing fermentation period (p<0.05), which indicates both peaks could be associated with fermentation metabolites.