Understanding how pomegranate cultivars respond to cold storage is essential for improving postharvest handling and minimizing quality deterioration. This study evaluated the postharvest performance and chilling tolerance of 12 commercially important Iranian pomegranate (Punica granatum L.) cultivars stored at 4°C ± 1°C with > 90% relative humidity for 120 days, followed by 3 days at room temperature to simulate shelf-life conditions. Fruit quality was assessed based on color attributes, biochemical characteristics, ripening indices, mineral composition, and physiological indicators associated with chilling injury. Significant cultivar-dependent differences were observed across all measured traits during storage. Red cultivars maintained higher a∗ values, whereas white cultivars exhibited higher L∗ and b∗ values. Substantial variation was also noted in total phenolic content, anthocyanins, antioxidant capacity, total soluble solids, and titratable acidity. Among the studied cultivars, “Malase Yazdi” and “Ardestanie Mahvalat” exhibited the highest chilling tolerance, whereas “Malase Saveh” and “Naderie Badroud” were the most susceptible. Chilling-tolerant cultivars were characterized by higher calcium content, lower electrolyte leakage and malondialdehyde accumulation, reduced polyphenol oxidase and peroxidase activities, and higher catalase activity. Overall, the results demonstrate strong genotype-dependent variation in postharvest behavior, with chilling tolerance closely associated with antioxidant capacity, mineral composition, and membrane stability.