The purpose of this research was to determine the effects of the packaging materials and size on the stability of monomeric anthocyanins, polyphenols, antioxidant activity, ascorbic acid, colour index and hydroxyl methyl furfural (HMF) during the 12-month shelf life of sour cherry nectars at 4 °C and 20 °C. Sour cherry nectars were aseptically filled out into packaging of different sizes and materials. The packaging included cartons of two different sizes (200 and 1000 mL) and aluminium cans (330 mL). Results showed that the nectars were of better quality when stored at lower temperatures. HMF generally increased significantly for all nectars during storage. Conversely, the total polyphenol content and the antioxidant activity of the nectars stored in aluminium cans and the larger-sized carton packaging decreased during storage. Lower anthocyanin loss and colour change were found in the nectars stored in aluminium cans. However, the better packaging material was found to be the large-sized carton package when HMF was analysed.