Considerable progress has been made in functionalization of the soy isoflavones through enzymatic modification of daidzin, genistin, and glycitin. After hydrolysis of $eta$-glucosides into their corresponding aglycones, these compounds were structurally modified via biotransformations such as regioselective hydroxylation, enantioselective reduction, regioselective methylation, and polymerization. These reactions often resulted in an increase of the biological activities (e.g., anti oxidative activity, antiproliferative activity) and/or improvement of the physico-chemcial properties (e.g., water solubility, bioavailability). This review briefly summarizes on-going research activities on the biofunctionalization of the soy isoflavones.