Abstract: The temperature sensitive differential of the solubilities of various isoflavone fractions is used to initially separate the fractions by heating an aqueous soy molasses or soy whey feed stream. The temperature of the feed stream is selected according to the temperature at which a desired isoflavone fraction or fractions become soluble. Then, the heated feed stream is passed through an ultrafiltration membrane having a cutoff which further selects desired isoflavone molecules by size. In some examples, the permeate is subjected to reverse osmosis in order to concentrate the solids. The resulting permeate is put through a resin adsorption process carried out in at least one liquid chromatography column to further separate the desired isoflavone fractions. A plurality of such columns may be used to provide a continuous process. Various processes are described for drying and crystallizing the isoflavone fractions.