The objective was to determine the effect of time and temperature on the concentration of bioactive compounds during germination of Brazilian soybean cultivar BRS 258. The concentration of bioactive compounds was optimized using Response Surface Methodology, with a 22 central composite rotational design and germination time and temperature as independent variables. Germination was carried out in a germination chamber, using paper in trays containing 500g of seeds. Germination temperature and time modified the concentrations of bioactive compounds within the ranges studied. An increase in germination time at 25°C decreased the concentration of Bowman-Birk inhibitor, lectin and lipoxygenase. After 63h of germination, a temperature increase from 20°C to 30°C resulted in a decrease of lipoxygenase activity by 22.5%. Optimal increases in the concentrations of isoflavone aglycones (daidzein and genistein) and saponin glycosides were observed with a 63h germination time at 30°C. Both germination time and temperature had an influence on the composition and concentration of bioactive compounds in germinated soybean flour. Equations determined can be used to predict concentrations of bioactive compounds in germinated soybeans in relation to climate changes and thus optimize their potential use in human health and nutrition. © 2009 Elsevier Ltd.