Enzymatic pretreatment of seeds is a novel approach that enhances the health benefits of the extracted oil. The study investigated the influence of the enzymatic pretreatment of seeds on the quality of oil from different pomegranate cultivars. The quality of the ultrasound-assisted (and ethanol-extracted) oil was studied, with respect to the refractive index (RI), yellowness index (YI), conjugated dienes (K232), peroxide value (PV) ρ-anisidine value (AV), total oxidation value (TOTOX), total carotenoid content (TCC), total phenolic compounds (TPC), fatty acid composition, phytosterol composition, ferric reducing antioxidant power (FRAP), and 2.2-diphenyl-1-picryl hydrazyl (DPPH) radical scavenging capacity. The seeds of three different pomegranate cultivars (‘Wonderful’, ‘Herskawitz’, and ‘Acco’) were digested with an equal mixture of Pectinex Ultra SPL, Flavourzyme 100 L, and cellulase crude enzymes, at a concentration, pH, temperature, and time of 1.7%, 4.5, 40 °C, and 5 h, respectively. Enzymatic pretreatment of PS increased oil yield, PV, TPC, TCC, and DPPH radical scavenging capacity, but decreased the YI. The levels of K232, AV and TOTOX, fatty acids, phytosterols, RI, and FRAP, were not significantly affected by enzymatic pretreatment of PS. Principal component analysis (PCA) established that oil extracted from the ‘Acco’ seed after enzymatic pretreatment had higher yield, TPC, TCC, and DPPH radical scavenging capacity. Therefore, enzyme-pretreated ‘Acco’ pomegranate fruit seed is a source of quality seed oil with excellent antioxidant properties.