Stem cells represent the regenerative capacity of our bodies; hence, it is essential for these cells to interact with the intrinsic and extrinsic environments, including nutritional components. Stem cells receive the nutritional elements as signal molecules that transmit certain messages to the cell epigenome, leading to cell differentiation. Such an effect could be similarly induced using several epigenetic modifiers. The influence of nutritional elements and contaminants on differentiation were demonstrated on embryonic stem cells during the embryonic development, as well as through in vitro studies. Similar evidence can be illustrated for adult stem cells in laboratory experiments. The interaction between nutrition and epigenetic can exert their effects on stem cell plasticity and differentiation, which may help in maintaining our health status and help in tissue regeneration after disease. This chapter includes an overview of the interaction between nutrition and stem cells through epigenetic mechanisms.