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The purpose of this research was to evaluate the effect of cold atmospheric pressure gas phase plasma treatment on anthocyanins and phenolic acids in sour cherry Marasca juice. Plasma treatment was optimized using a response surface methodology regarding the treatment time, sample volume and applied gas flow and compared to thermal pasteurization and untreated juice. Short treatment (3 min) of larger volume of the juice (3 mL) resulted in the highest concentration of both anthocyanins and phenolic acids. Compared to pasteurized and untreated juice, plasma treated sour cherry Marasca juice at optimized conditions had higher amount of phenolic compounds. Observed increase in phenolic compounds content in sour cherry Marasca juices could be a result of undefined small-sized aggregates or particles, which would be dissociated by the plasma treatment.