Both the blueberry fruits and whole juice presented good stability with respect to their antioxidant capacity during cold storage, after remaining frozen for a long period and under refrigeration for shorter periods, with little loss of their antioxidant properties. On the other hand, there were significant losses of anthocyanins, possibly due to oxidation and/or condensation reactions with other phenolic compounds. This difference allowed for the inference that the other phenolic compounds, or an association of these with the anthocyanin degradation products, were responsible for maintaining the antioxidant activity and even increasing it during storage. Nevertheless, preventative measures, such as prior blanching and/or the use of vacuum packaging, are recommended. However, further studies are required in order to optimize the storage time and temperature for such products in relation to their functional properties, as also to identify the compounds formed by the co-pigmentation phenomenon, since they are probably compounds with high antioxidant activity.