Controlled atmosphere (CA) storage has been observed to prolong the shelf life of fresh produce. The objective of this study was to determine whether CA storage performed better than regular air (RA) storage in maintaining fruit quality of six pomegranate (Punica granatum L.) cultivars grown in the state of Georgia. Pomegranate fruit produced in Ty Ty, GA in 2010 and 2011 were stored in CA [5% CO2 + 3% O2, 5 °C, 90% to 95% relative humidity (RH)] or RA (5 °C, 90% to 95% RH) for 3 months. Pomegranate whole fruit and juice were evaluated for various physical and chemical attributes at the end of storage. Fruit differed by cultivar for rind smoothness, fruit cracking, disease incidence, and chilling injury (CI). Fruit stored in CA had a smoother and less shriveled rind, lower CI, fewer disease severity symptoms, and thus better quality than fruit stored in RA. Fruit rind color, total soluble solids (TSS), titratable acidity (TA), and anthocyanin content in fruit juice were unaffected by storage method. The results showed that pomegranate fruit quality was better sustained under CA compared with RA storage.