Traditionally fermented soybeans (chungkookjang; TFC) may have potent anti-diabetic activity, depending on the ambient microorganisms and conditions. We hypothesized that one of the major Bacillus species in TFC contributes to the anti-diabetic activity and could be used to standardize a highly functional TFC. We tested the hypothesis by using cell-based studies to evaluate insulin sensitizing and insulinotropic action of chungkookjangs fermented with various Bacillus spp. and fermentation periods. The 70% methanol and water extracts of chungkookjang fermented with Bacillus licheniformis (BL) for 48 h contained similar profiles of isoflavonoids and peptides to methanol and water extracts of TFC with potent anti-diabetic activity. Water extracts (mainly containing peptides) of TFC and BL fermented for 48 h and 72 h had a better insulin sensitizing action via activating peroxisome proliferator-activated receptor-γ (PPAR-γ) and increased the expression of PPAR-γ in 3T3-L1 adipocytes better than unfermented cooked soybeans (CSB). The 70% methanol extracts (predominantly isoflavone aglycones) of BL fermented for 48 h and 72 h improved glucose-stimulated insulin secretion and protected β-cell viability better than CSB in insulinoma cells, and the improvement by BL was similar to TFC. In conclusion, the BL water extract fermented for 48 h exhibited equal insulin sensitization as TFC and BL methanol extract exerted similar insulinotropic actions to those of TFC. B. licheniformis may be one of the major microorganisms responsible for anti-diabetic actions of chungkookjang. It is important to make chungkookjang that retains the anti-diabetic properties of the most efficacious traditional chungkookjang using a standardized method.