Scientific advancements in recent years have shed new light on the relationship between diet and human health. Nutrients play an important role in the prevention of many civilization diseases, such as osteoporosis, type II diabetes, hypercholesterolemia, and cardiovascular diseases. The biological activity of natural plant components allows their use in the treatment of various diseases, especially civilization diseases, to be speculated. Special attention is paid to phenolic compounds that have numerous health-promoting properties. Isoflavones, phenolic compounds, are commonly found in legumes, especially in soybeans. Their structural similarity to 17-β-estradiol (E2), the main female sex hormone, allows them to induce estrogenic and antiestrogenic effects by binding to estrogen receptors, and their consumption has been associated with a decreased risk of hormone-related cancers. In addition, numerous epidemiological studies and related meta-analyses suggest that soy consumption may be associated with a lower incidence of certain diseases. However, there are some doubts about the potential effects on health, such as the effectiveness of cardiovascular risk reduction or breast cancer-promoting properties. The purpose of this review is to present the current knowledge on the potential effects of soy isoflavone consumption with regard to civilization diseases.