This study aimed to extract bioactive compounds from apple (Malus domestica) peel waste using supercritical CO2 extraction. The bioactive fractions from apple peels from the three Italian cultivars were extracted applying a temperature of 60 °C and a pressure of 250 bar for 15 min. 20% ethanol was used as a co-solvent. The extraction process was carried out at a flow rate of 2 mL/min and their total polyphenol (TP), anthocyanin (TA), ascorbic acid (AA), and antioxidant activity contents (TAC) were measured. The extracts from the Stark cultivar had the highest levels of polyphenols, anthocyanins, and ascorbic acid, while the Royal Gala cultivar had the highest total antioxidant activity. Chromatographic analyses were also performed to characterize polyphenols. The extracts were then tested for their effect on the mitochondrial NADH-ubiquinone oxidoreductase (Complex I) activity on mitochondria isolated from human embryonic kidney cells (HEK239) cells, with the Stark extracts showing the most positive response in terms of NADH oxidation. These findings highlight the potential of apple peel waste as a source of functional phytocompounds and suggest the Stark cultivar extracts may have pharmacological applications. This study supports the circular bioeconomy by promoting the use of waste products as a valuable resource.