Pulsed electric fields have the potential to be used as alternative to other conventional techniques of food production. In the last few years, several studies have demonstrated the ability of intense treatments to obtain safe and shelf-stable liquid foods. On the other hand, novel applications such as improvement of mass transfer processes or generation of bioactive compounds by using moderate field strengths are under current development. However, the effects of pulsed electric field treatments on minor constituents of foods, namely on bioactive compounds, have not been always considered. This review aims at updating the state of the art regarding the impact of pulsed electric field processing conditions on the stability of bioactive compounds in food systems.