Effect of lactic acid bacteria-fermented whey in the soybean soaking process of the soymilk production was investigated to minimize bacterial contamination and increase isoflavone and ${gamma}$-amino butyric acid (GABA) concentrations. Mixed culture of Lactobacillus acidophilus, Bifidobacterium lactis, and Streptococcus thermophilus displayed the highest ${eta}$-glucosidase activity and was used for the production of health functional soymilk. A significant pH reduction from 6.75 to 5.19 was observed in soymilk product, whereas its titratable acidity increased from 0.18 to 0.24% after 24-h soaking of soybean in fermented whey. Suspension stability of soymilk dramatically dropped between 18- and 24-h soaking periods, largely due to pH reduction, which reflected decrease in solid contents of soymilk from 7.38 to 1.54%. Total isoflavone content significantly decreased with increasing soaking time in the fermented whey, whereas the content of health-beneficial aglycone increased by three fold (0.27 mg/100 mL of soymilk) after 18-h soaking fermentation. The contents of free amino acids (6.0 mg${ ightarrow}$2.3 mg/100 mL) and GABA (1.1 mg${ ightarrow}$0.5 mg) in soymilk were reduced in soymilks produced with the fermented soybeans between 18- and 24-h soaking periods. The pH-drop induced solid precipitation, which could exert negative effect on the free amino acid and GABA contents in fermented soymilk.