Pomegranates are a well-known source of valuable substances with high antioxidant capacity. The manufacturing of pomegranate juices and their storage produce relevant changes on physical, chemical, and phytochemical composition of pomegranates. Pasteurization (thermal treatment) is the most popular preservation technique; however, new approaches (non-thermal ones), such as UV-C irradiation are being considered to produce high-quality food. Pomegranate juices have shown higher antioxidant capacity (~. 20%) than squeezed arils due to the migration of phenolic compounds from the rind while pressing the fruits. The main compounds responsible for the antioxidant capacity of pomegranate juices are punicalagins, hydrolysable tannins, anthocyanins, and ellagic acid. In general, while processing punicalagins increased but ellagic acid decreased. Anthocyanins are associated to both fruit and juice color and antioxidant capacity, and their concentration decreases during processing. The flavor of pomegranates is characterized by esters, alcohols, and terpenes, while after juicing and pasteurization compounds such as furans and sesquiterpenes increase.