Cheonggukjang is a traditional Korean fermented soybean food with potential health benefits. For this reason, Cheonggukjang is consumed in the form of pills in addition to being used as a food ingredient. There are few clinical studies that have evaluated changes in various health indicators through blood and stool tests before and after consumption of Cheonggukjang. In this study, symptoms and hematological changes were analyzed before and after the intake of traditional Cheonggukjang pills containing high-dose (n =19) or low-dose (n =20) beneficial bacteria and commercial Cheonggukjang pills (n =20). Anti-obesity effects and body composition changes were determined before and after Cheonggukjang consumption. Lastly, the changes in microorganisms and short-chain fatty acids in the stool were compared. No changes in obesity and inflammation-related indicators were observed before and after Cheonggukjang consumption. TheFirmicutes/Bacteroidetesratio, associated with obesity, decreased in all three groups after Cheonggukjang consumption, but no statistical significance was indicated. Cheonggukjang contained various BAs, but they did not adversely affect symptoms and hematological changes in the participants. BAs generated during the manufacturing process of Cheonggukjang did not have any adverse effects in this randomized, double-blind clinical trial. Further research is needed in future concerning the anti-obesity effect or regarding changes in the microbiome and short-chain fatty acids in feces.