The present invention provides a process using a zeolite or molecular sieve for recovering isoflavones from aqueous mixtures, such as soy whey and other biological waste products. A zeolite, such as a large pore, hydrophobic zeolite, has a significantly higher affinity for isoflavones than conventional polymeric adsorbents, and has essentially no affinity for the undesired oligosaccharides raffinose and stachyose.