The aim of this study is to investigate the changes in the quality characteristics of cheonggukjang made with germinated soybeans, which is produced by the addition of a smoking process. The L value of smoked cheonggukjang made with germinated soybeans (SCGS) was higher than that of non-smoked cheonggukjang made with non-germinated soybeans (NCNS) and non-smoked cheonggukjang made with germinated soybeans (NCGS). The a value of NCNS was the highest, followed by NCGS and SCGS. The b and △T values had a similar tendency compared with the L value. The amino acids in NCGS were significantly decreased compared with NCNS, whereas no remarkable difference in amino acid content was observed between NCGS and SCGS. The moisture content of NCGS (61.9 ± 0.9%) was increased by more than 8% compared with that of NCNS (53.3 ± 0.7%). The moisture content of SCGS was significantly decreased compared with NCGS, whereas the moisture content of SCGS was higher than that of NCNS. The pH of SCGS was significantly the highest, followed by NCGS and NCNS. The viscous substance content of NCGS was significantly increased compared with that of NCNS. No remarkable difference in viscous substance content was observed between NCGS and SCGS. The number of aerobic bacteria in SCGS was significantly decreased compared with NCGS. The levels of total isoflavone in NCNS, NCGS, and SCGS were 1573.9 ± 62.5, 1759.1 ± 65.8, 1738.0 ± 68.1 mg%, respectively. The total organic acid content of smoked cheonggukjang made with germinated soybeans (SCGS) was four times higher than that of non-smoked cheonggukjang made with non-germinated soybeans (NCNS). The total organic acid content of SCGS was lower than that of non-smoked cheonggukjang made with germinated soybeans (NCGS). The total free sugar content of NCGS and SCGS was approximately three times higher than that of NCNS. The total free amino acid content of NCGS was significantly decreased compared with that of NCNS, whereas the total free amino acid content of SCGS was 1.2 times higher than that of NCGS. The essential amino acid content of SCGS was significantly increased compared with that of NCGS. The ratio of glutamic acid to the total free amino acid in NCNS and SCGS was 19.6%. Similarly, the ratio of glutamic acid to the total free amino acid in NCGS was 19.1%. There were no significant differences in the total fatty acid content of NCNS, NCGS, and SCGS. The sensory evaluation of appearance, aroma, taste, and overall quality of SCGS was significantly increased compared with that of NCNS and NCGS. These results suggest that smoked cheonggukjang made with germinated soybeans could be utilized for the development of a novel fermented food.