Sour cherry (Prunus cerasus L.) is rich in polyphenols, and like its processed products, is especially rich in anthocyanins. We have applied HPLC, spectrophotometric and on-line antioxidant detection methods to follow the fate of cherry antioxidants during an entire multi-step industrial-scale processing strategy. This was performed for 22 sampling points, with five independent repeats from a commercial cherry nectar production process. Anthocyanins contributed to >50% of the total antioxidant capacity of the samples. An in vitro gastrointestinal (GI) digestion system was used to investigate serum availability of antioxidants. In this system anthocyanin bioavailability was much higher in the processed nectar than in the fresh fruit. Together these results indicate that processed sour cherry nectar is a rich source of stable antioxidants with high bioavailability, auguring well for the potential health-promoting capacity of sour cherry products.