The changes in the β-glucosidase activity, total phenolic contents, isoflavone contents, and antioxidant activities during the fermentation of cheonggukjang by Bacillus amyloliquefaciens MJ1-4 with and without garlic were investigated. The levels of total phenolic and isoflavonemalonylglycoside, -acetylglycoside, and -aglycone contents increased, whereas the 2,2-diphenyl- 1-picrylhydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging activities and ferric reducing/antioxidant power (FRAP) assay results increased, but isoflavone-glycoside levels decreased during cheonggukjang fermentation. The levels of total phenolic and total isoflavone contents and the antioxidant activities were higher in cheonggukjang fermented without garlic (CFWOG) than in cheonggukjang fermented with garlic (CFWG) after 24 h of fermentation, but they were lower in CFWOG than in CFWG after 72h of fermentation. In particular, the highest levels of total phenolic, daidzein, glycitein, and genistein were present at concentrations of 15.18 mg/g, 264.4 μg/g, 16.4 μg/g, and 31.1 μg/g after 72h of fermentation in CFWG, showing 82.89% in DPPH radical scavenging activity, 106.32% in ABTS radical scavenging activity, and 1.47 (OD593 nm) in FRAP assay, respectively. From these results, we suggest that the high antioxidant activity of CFWG might be related to the markedly higher levels of total phenolic contents, isoflavone-malonylglycosides, - acetylglycosides, and -aglycones achieved during fermentation.