Clarification process gave as result an increase of antioxidant activity of pomegranate juice as consequence of reducing the antagonistic interactions between different antioxidant constituents. Thermal treatments here used (LTP and HTP) decreased the percentage of polymeric anthocyanin form, increasing on the contrary the monomeric one in pomegranate juice. Additionally, pasteurizations had not influence on the TPC and antioxidant capacity of juices. Storage temperature was, however, the main factor affecting all the parameters tested (total monomeric and individual anthocyanins, TPC, and antioxidant activity). Fast degradation of anthocyanins was observed in juices stored at 25 °C, while refrigerated storage (5 °C) resulted in much lover degradation rate. Cy3G was more instable than Dp3,5dG and Cy3,5dG, and consequently its normal dominance in juice from arils of ‘Mollar’ pomegranates was altered in favour of diglucoside anthocyanins. A linear relationship was observed between ORAC values and total monomeric anthocyanins, suggesting that they contributed strongly to the antioxidant capacity of juice. Results presented in this study show that hurdle technology (heat treatment plus refrigeration) may help to reduce anthocyanin degradation in pasteurized pomegranate juice, avoiding a dramatic impact on its colour and preserving the antioxidant capacity and beneficial effects of this specific bioactive compounds on human health.