Ready-to-eat pomegranate arils are considered a “functional food” for their health benefits and have desirable sensory characteristics, which have caused an increasing interest by the consumers for this product. The preparation process of ready-to-eat fruit products can cause severe injuries and worsen their quality and shelf life significantly. Modified atmosphere packaging (MAP) has been used broadly in the last years to maintain the quality of processed fruits and showed optimal results, in spite of the possible problems caused by the depletion of O2 and corresponding accumulation of CO2 in the package. This study was conducted to evaluate the effects of different MAP treatments, based on nitrogen or alternatively on a noble gas, argon, in combination with refrigerated storage (0, 4, 8, 12, and 16 days at 4 ± 1 °C and 90 ± 5% RH) on the qualitative parameters of pomegranate arils with the aim to prolong their post-harvest life maintaining the original quality. The argon-based MAP treatment (MAPAr) was the one that provided the best results, assuring a limited loss of weight and juice content. The use of noble gas allowed to maintain a high sugar/acid ratio until 16 days from packaging. Sensory analysis on all MAP treated arils and, on the juice, obtained from them were carried out, and judges showed a preference for MAPAr treated arils and juice until day 12 from packaging.