The objective was to optimise the effect of germination time and temperature on the concentration of soluble protein, lunasin, BBI, lectin, saponins and isoflavones in soybean seeds from cultivar BRS 133. Isoflavone and saponin concentrations were analysed by HPLC. Lunasin, Bowman-Birk inhibitor and lectin were analysed by ELISA and western blot. The effects of the variations in germination time and temperature on bioactive compounds were analysed using the response surface methodology (RSM), with a 22 central composite rotational design. Germination of soybean for 42 h at 25 °C resulted in an increase of 61.7% of lunasin, decrease of 58.7% in lectin and 70.0% in lipoxygenase activity. Optimal increases in the concentrations of isoflavone aglycones were observed in combination of 63 h of germination and 30 °C. A significant increase of 32.2% in the concentration of soy saponins was observed in combination of 42 h of germination at 25 °C. © 2009 Elsevier Ltd. All rights reserved.