The consumption of soybeans and their constituents, isolated soy protein and isoflavones, has been associated with positive effects on body weight, lipid profile and insulin, which has stimulated the production and consumption of foods derived from soy. However, these polyphenolic compounds (isoflavones) have similar structure to 17-β estradiol and may act as agonists or antagonists in estrogen receptors. Due to its estrogenic activity, the safety of its consumption during critical periods of development, such as gestation and lactation, has been questioned. Studies that evaluate the effects of soybeans on endocrine metabolic parameters are still controversial. This review focuses on the role that soy and isoflavones play during critical periods of development and into adulthood.