In this study sour cherry pomace was extracted with food-grade solvent (50% ethanol), concentrated and stabilized in whey and soy proteins by encapsulation. Soy proteins exhibited higher encapsulation efficiency (94.90%), but not significantly (p < 0.05), from whey (90.10%). Storage properties of whey (WP) and soy protein (SP) encapsulates in terms of total polyphenols, anthocyanins and antioxidant activity were tested for 6 weeks. At the end of storage period the retention of polyphenols in SP and WP was similar (67.33 and 69.30%, respectively), while the content of anthocyanins has increased in SP (for 47.97%) and decreased in WP (for 1.45%). The decrease in antioxidant activity in SP (12.22%) was lower than in WP (35.04%). Colour parameters of encapsulates have followed the similar trend as anthocyanin change during storage. The technique reported herewith can be used for obtaining quality encapsulates for their use as functional food additives, as a way of fruit waste valorization.