An increase in the production rate of cherry and cherry products has led to considerable amounts of waste that accumulates rapidly especially during the harvest season. The waste including pits is used as fuel, fertilizer, and partly discarded in the environment. Although the cherry fruit is shown to be a rich source of polyphenols, there is limited information about the polyphenol content of the waste, especially the pits. This study aims to integrate a sequence of novel processing technologies (extraction and encapsulation) for the valorization of cherry pits, i.e. turn them into valuable antioxidant products that can be used in healthcare, cosmetics, and packaging applications. The operative parameters of the extraction process to obtain the maximum polyphenols and encapsulation to protect the extracts were optimized. The results of this study confirmed the feasibility of the extraction and encapsulation to recover a notable concentration of polyphenols with enhanced antioxidant properties. These antioxidants can be used as antibacterial compounds to develop active packaging.