The present invention provides a process using zeolites for recovering isoflavones and removing undesired oligosaccharides from aqueous mixtures, such as soy whey and other plant processing waste products. The aqueous mixture is treated with a large pore hydrophobic zeolite, such as zeolite Beta, to remove isoflavones, followed by treatment with an ultrastabilized, hydrophobic zeolite Y, such as CBV-901 or HiSiv.TM. 4000, to remove the undesired oligosaccharides raffinose and stachyose. The recovered isoflavones and digestible sugars, glucose, sucrose, and fructose, are useful in food products.