Isoflavones belong to a group of compounds known as flavanoids that share a basic structure consisting of two benzene rings linked through a heterocyclic pyrane C ring. Soybean provides the most abundant source of isoflavones, which have been linked to the prevention of several diseases, including cancer (prostate, colon, and breast cancer), hypercholesterolemia, cardiovascular disease, atherosclerosis, osteoporosis, and relief of menopausal symptoms in certain women. Currently, isoflavone use is targeted as a nutraceutical. In this article, we review the structural aspects and the effect of processing on the different forms of isoflavones in soy protein. We also discuss the impact of these changes on the health benefits of eating foods containing isoflavones. Isoflavones, as a class of phytoestrogens, are gaining a lot of interest in clinical nutrition.