The processed juice (or nectar) of the sour cherry, Prunus cerasus L., is widely consumed in the Balkan region and Turkey. Sour cherry is known to be rich in polyphenolic compounds, such as anthocyanins and procyanidins. In this work, the effects of processing of sour cherry fruit to nectar on polyphenolic compounds was studied. From a Turkish industrial nectar production factory, five fruit batches were sampled during the processing from fruit to nectar, and for each batch 22 sampling points in the process were investigated. Untargeted LC–MS analysis revealed 193 compounds in sour cherry, of which 38 could be putatively identified. Only seven compounds were affected by the process from fruit to nectar, among which were five phenolic compounds. Waste residues such as press cake contained hardly any anthocyanins, while 87% of the major fruit anthocyanin, cyanidin-3-(2G-glucosylrutinoside), was found in the final nectar. In contrast, procyanidins showed a lower recovery (62%), and were still well represented in the discarded press cake. In comparison with other fruit juices, the recovery of anthocyanins in sour cherry nectar is remarkably high.