Blueberries are highly perishable fruits, and consequently, storage under high CO2 and low O2 levels is recommended to preserve the highly appreciated polyphenols. However, high CO2 levels might be detrimental for certain cultivars. The aim of this study was to investigate the impact of storage conditions on various quality parameters, including polyphenol composition in 'Duke' berries. Results show that storage under 18 kPa CO2, coupled with 3 kPa O2, resulted in accelerated softening of berries, which was accompanied by lower levels compared to other conditions of hexosides and arabinosides of malvidin, petunidin, cyanidine, and delphinidin. However, this storage condition had no negative impact on chlorogenic acid levels. Expression data of key polyphenol-biosynthesis genes showed higher expression levels of all investigated genes at harvest time compared to all storage conditions. Of particular importance is the expression level of chalcone synthase (VcCHS), which is severely affected by storage at 18 kPa CO2.