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Sweet cherries are processed in various ways, leading to significant amounts of underutilized by-products that can potentially be used as a source of bioactive compounds, including antioxidants. The present study focuses on identifying ways to exploit bioactive compounds from sweet cherry skins, namely the extraction, microencapsulation, and functionalizing of some food product to obtain added value. The anthocyanins from skins were extracted and encapsulated in a combination of whey proteins isolate and chitosan by freeze-drying, with an encapsulation efficiency of 77.68 ± 2.57%. The powder showed a satisfactory content in polyphenols, of which anthocyanins content was 14.48 ± 1.17 mg cyanidin 3-glucoside/100 g dry weight (D.W.) and antioxidant activity of 85.37 ± 1.18 µM Trolox/100 g D.W. The powder was morphologically analyzed, revealing the presence of coacervates, ranging in size from 12–54 μm, forming large spheresomes (up to 200 μm). The powder was used as a functional ingredient to develop two value-added food products, namely yoghurt and marshmallows. The powder was tested for its prebiotic effect on L. casei 431^® in the yoghurt samples during 21 days at 4 °C, when a decrease in viability was found, up to 6 log CFU·g⁻¹. The anthocyanins and antioxidant activity decreased in yoghurt and increased in marshmallows during storage time. The obtained results support the potential use of extracts from underutilized sources in the development of functional ingredients and value-added food products.