Isoflavones, phenolic compounds with a 3-phenylchromen-4-one backbone, are plant-derived metabolites found primarily in the Fabaceae family. Hundreds of isoflavone structures have been identified so far. Regarding human nutrition, the most important of these are soybean isoflavones including daidzein, genistein, and glycitein. After ingestion, isoflavones are deglycosylated, demethylated, oxidized (or reduced), glucuronidated, or sulfated by enterocytes, liver cells, and intestinal microorganisms. Among the metabolites, daidzein metabolite equol has the greatest impact on human health. Due to their similarity to estrogens, equol and genistein, and to a lesser extent other isoflavones, exert estrogenic or antiestrogenic effects in mammals, leading to antimenopausal, cardioprotective, antiosteoporotic, and in the case of estrogen-related cancers, anticarcinogenic effects. Apart from these hormone-related activities, isoflavones possess antioxidant properties and influence several other biological processes. However, the health effects of food-derived isoflavones are dependent on the food matrices and also on the ability of intestinal microflora to produce equol. For the individuals who cannot produce equol, the consumption of milk is an alternative, as significant amounts of this metabolite are excreted into milk in cows fed feedstuffs rich in isoflavones. Thus, targeted cattle nutrition could result in the production of milk that can be considered a functional food.