Sour cherry (Prunus cerasus L.), has gained growing interest in recent years due to the envisaged health benefits associated with a regular intake of anthocyanins and related polyphenolic compounds. Turkish sour cherries are widely consumed as processed products and are renowned for their high juice quality. However, the phytochemistry of anthocyanins and other flavonoids in processed sour cherry products is still unclear. In the present study, we aim to investigate the effects of processing sour cherry fresh fruit to the final juice product on the content of anthocyanins and other related polyphenols. ‘Kutahya’, a local sour cherry cultivar, was processed to juice at laboratory scale using 5 different batches. The changes in moisture content, sugar content (qualitative and quantitative), procyanidin content and vitamin C content during processing were analysed. Furthermore, LC-QTOFMS/ MS based metabolomics and HPLC analyses were performed for the identification and quantification of individual anthocyanins and related polyphenols. Comparisons of processing samples based on either wet-weight or dry-weight were complicated by evaporation steps and addition of sucrose syrup. Studies on procyanidin content showed that the mash heating, mash pressing and first pasteurization of raw juice steps resulted in an increase in procyanidins, while final juice samples were found to have significantly lower procyanidin contents on a dryweight basis. The procyanidin profile was found to be dominated by short-chain polymers with an average chain-length of 2 monomer units. The major anthocyanin compound was cyanidin 3-(2G-glucosylrutinoside) followed by cyanidin 3-rutinoside which all showed an increase in content after the mash pressing step and a decrease on processing to final juice.