Pomegranate cultivar 'Wonderful' fruit are susceptible to storage-induced chilling injuries of the peel (CIp), appearing as superficial browning of the skin, the outer colored layer of the peel. Skin quality can be divided into 3 categories: high quality (HQ) - skin, smooth, shiny with an intense red color; CIp - skin with dark brown regions; and husk scald (HS) - skin with a brownish tint and peel hardening. To explore the dynamics of CIp development in relation to the time of harvest, fruit were collected at the beginning of the first week (FW) and at the end of the last week (LW) of harvest. After 1.5, 3, and 4 months in storage, fruit were sorted into HQ-, CIp- and HS-skin types. Results indicated a significant reduction in HQ-fruit percentage and an increase in CIp- and HS-fruit after 3 months in storage. Up to 3 months, there was no significant change in skin quality; however, the percentage of HQ-fruit differed between FW- and LW-fruit and was higher in the former. Expression of genes related to antioxidative response (CAT2, SOD, GR2), superficial browning (PPO, PAL), and anthocyanin biosynthesis (CHS, CHI, DFR) suggested that an increased expression of CHS, CHI, and DFR during storage together with low expression of PPO may contribute to skin resistance against the cold stress and reduced CIp development. PPO, SOD, and GR2 were upregulated in the skin due to CIp development. It is suggested that the ability to accumulate anthocyanins during the storage may contribute to skin resistance against prolong cold stress, and spectral analysis of fruit skin color following short storage may enable to predict whether the fruit can be kept for longer storage time.