Changes in β-glycosidase, esterase activities, isoflavone, flavanols and phenolic acid during the fermentation of Korean whole soybean fermented food cheonggukjang by Bacillus pumilus HY1 were investigated. The levels of aglycones, flavanols and gallic acid increased, while the β-glucosidase activity, esterase activity, glycosides content (except for acetylglycosides) and flavanol gallates decreased. Total isoflavone content slightly decreased after 60 h of fermentation, while total flavanol and phenolic acid content increased. The highest levels of daidzein (aglycone type) and acetyldaidzin (glycoside type) were recorded after 48 h of fermentation. The levels of catechin, epicatechin and gallic acid also increased during fermentation. However, total contents of glycosides, malonylglycosides and flavanol gallates decreased by about 80%, 90% and 60% during 60 h of fermentation, respectively. In addition, total phenolic content increased markedly during fermentation, while levels of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging activity increased. Hence, it would be beneficial for the food industry if components of cheonggukjang could be separated and developed into functional products.