Weight loss and decay are common physiological disorders during postharvest handling and storage of pomegranates. The study focused on relating the ability of plastic liners as internal packaging to modify both gaseous and moisture atmosphere around the fruit to moisture dynamics and physical and physiological quality of pomegranate fruit (cv. Wonderful) during storage. Fruit were packed with no-liner, non-perforated ‘Decco’, non-perforated ‘Zoe’, micro-perforated Xtend®, 2 mm macro-perforated high density polyethylene (HDPE), and 4 mm macro-perforated HDPE plastic liners. After 84 days of storage at 5 °C and 90–95% relative humidity (RH), fruit packed with no-liner lost 15.6 ± 0.3% of initial weight. Non-perforated (Decco and Zoe) liners minimised losses to 0.79 and 0.82% compared to Xtend® micro-perforated (4.17%) and 2 mm HDPE (2.44%) and 4 mm macro-perforated HDPE (4.17%) liners, respectively. Clearly, micro- and macro-perforation of liners minimised moisture condensation, fruit decay, and shrivel severity. Micro-perforated Xtend® and macro-perforated 4 mm HDPE were the best treatments in minimising postharvest losses that are often associated with inadequate environment control inside packaging compared to the use of non-perforated liners.