Pomegranate exhibits important postharvest quality losses that limit its storage potential, caused mainly by weight loss, chilling injury and fungal diseases. In this work, we evaluated the effect of novel hydroxypropyl methylcellulose (HPMC) edible coatings (ECs) formulated with three different lipids (beeswax (BW), carnauba wax, and glycerol monostearate), as hydrophobic components, and two different GRAS salts (potassium bicarbonate (PBC) and sodium benzoate (SB)), as antifungal ingredients, to control weight loss and natural fungal decay of ‘Mollar de Elche’ pomegranates during storage at 20 °C. Afterwards, selected antifungal ECs and commercial modified atmosphere packaging (MAP) films were assayed alone or in combination to control natural decay and preserve fruit quality of pomegranates stored at 5 °C for 4 months plus 1 week at 20 °C. Results showed that ECs amended with SB reduced pomegranate latent infections caused by Botrytis cinerea and wound diseases caused by Penicillium spp. Moreover, MAP technologies were confirmed as an efficient mean to preserve freshness, prevent fruit shriveling and rind browning, and reduce fungal decay, thus extending storage life of pomegranates. The combination HPMC-BW-SB + MAP was the most promising treatment as it reduced weight loss and decay, without negatively affecting the fruit physicochemical and sensory quality.