Isoflavones occur primarily as glycosides (namely, malonyl-, acetyl-, and non-conjugated beta-glycosides) and a small percentage as the bioactive aglycon. The different chemical structures of isoflavones can dictate their stability during processing. Therefore, our objective was to determine the effects of pH and thermal treatments on conjugated isoflavones with regard to interconversions and loss. Conjugated daidzin and genistin were heated at 25, 80, and 100 degrees C under neutral, acidic, and basic conditions. Changes in isoflavone derivatives were monitored using high-performance liquid chromatography. Along with interconversions, considerable loss in total known isoflavone derivatives was noted for each isoflavone, especially under elevated pH and temperature. The malonylglycosides showed more stability than acetylglycosides, especially under acidic conditions. Overall, loss in isoflavone derivatives was significantly higher for daidzin than for genistin glycoside forms. Our results highlighted the significance of chemical structure with regard to stability, which is a key factor in determining soy processing conditions.