A new process was developed for the production of pre-cooked whole soybeans with high concentration of isoflavone aglicones. The process is based on the adjustment of the rate of water uptake by controlled hydration, followed by an incubation period prior to the heat treatment in order to maximize hydrolysis of isoflavone glucosides into their respective aglicones in the pre-cooked soybeans. For the development of the process it was first necessary to evaluate the effect of the various operational variables (extent of hydration, temperature, rate of water absorption and duration of hidrolysis) on the isoflavone profile of the processed beans. Using the controlled hydration process under optimized conditions (54 ºC/ 15 rpm) it was possible to substantially increase the total amount of isoflavone aglicones present in the soybeans. After the desired level of moisture was reached, the beans were incubated in order to allow the endogenous enzymatic hydrolysis to occur thus increasing amount of isoflavone aglicones. A mild thermal treatment (120 ºC/5 minutes, 1 kg.cm-2) was sufficient to improve sensory characteristics but was not fully effective to promote hydrolysis of the isoflavone glycosides. Overall conversion of the isoflavone glycosides to aglycones was superior to 65% and no losses by leaching into the hydration water were detected. The total isoflavone aglycones content increased from 10.23 µg.g-1 in the raw material, to 283.34 µg.g-1 in the processed soybeans. Worthy of notice was the unusually high increase in daizein, particularly in relation to genistein, thus suggesting the influence of individual substrate-dependent modes of action of the endogenous enzymes. It is concluded that by controlling the hydration of soybeans prior to pre-cooking, substantial increases of endogenous hydrolysis of isoflavone glucosides can be obtained resulting in the augmented delivery of metabolizable aglycones of pre-cooked products