In our study, lactic acid bacteria (LAB)-fermented whey solutions were applied in the soybean soaking process to minimize bacterial contamination and to enrich the biologically functional components of isoflavone and $gamma$-aminobutyric acid (GABA). Among the 11 LAB tested, Bifidobacteria infantis and a mixed culture (Lactobacillus acidophilus, Bifidobacteria lactis, and Streptococcus thermophilus; ABT-3) displaying the greatest $eta$-glucosidase activity were selected to produce improved biologically functional soybean preparations. In the soybean soaking processing (without water spraying), the LAB-cultured 10% whey solution was used to soak and to ferment the soybeans and the fermented soybeans were finally dried by heat-blowing at $55^{circ}C$. The processing conditions used in this study demonstrated that the final soybean product had a reduced contamination by aerobic and coliform bacteria, compared to raw soybeans, likely due to the decrease in pH during LAB fermentation. The aglycone content of the isoflavone increased up to 44.6 mg per 100 g of dried soybean by the processing method, or approximately 8-9 times as much as their initial content. The GABA contents in the processed samples increased as the processing time of soaking-fermentation proceeded as well. The soybean sample that fermented by ABT-3 culture for 24 hr showed the greatest increase in GABA content (23.95 to 97.79 mg/100 g), probably as a result of the activity of glutamate decarboxylases (GAD) released from the soybean or produced by LAB during the soaking process.