Soy isoflavones are bioactive compounds that can benefit human health and occur in four distinct chemical classes of structures: β-glucosides, 6”-o-malonylglucosides, 6”-o-acetylglucosides, and aglycones. The soaking of soybean is a process used previously for the preparation of various soy products and promotes the migration of isoflavones to the soaking solution, which is generally discarded after this step. The objective of this study was to investigate the effect of hydrothermal treatment on the loss of soybean isoflavones to the soaking solution using central composite design (CCD). The soybean grains were soaked (1:1.5, w/w, soybean: 0.05 M citrate-phosphate buffer solution pH 6.0) under different time (3.17, 4.00, 6.00, 8.00, and 8.83 h) and temperature (40.86, 45.00, 55.00, 65.00, and 69.14 °C). The linear, linear and quadratic effects of variables soaking time and temperature, respectively, were significant (p < 0.05) and positive on the concentration of β-glucosides in soaking solution, and the maximum concentration (11.41 mg /100 mL) was estimated in 8.83 h at 69.14 °C. At this temperature was estimated maximum concentration of malonylglucosides (57.06 mg /100 mL) in the soaking solution independent of soaking time. The time and temperature of soaking of soybeans showed a positive linear and negative quadratic effect on the concentration of aglycones in the soaking solution, with maximum content (0.64 mg /100 mL) in 8.83 h at 55 °C. The hydrothermal treatment of soybeans promotes the formation of aglycones in soaked grain and to minimize leaching of isoflavones is necessary to use proper ratio soybean: soaking solution.