Microwave pretreatment of oilseeds is a novel technique used to enhance oil nutraceutical properties. In this study, the effect of microwave pretreatment of seeds was investigated on pomegranate seed oil quality attributes including oil yield, yellowness index, refractive index, peroxide value, ρ-anisidine value, total oxidation value, conjugated dienes, total phenolic content, total carotenoids content, phytosterol composition, fatty acid composition, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity, and ferric reducing antioxidant power (FRAP). The seeds of three different pomegranate cultivars (‘Acco’, ‘Herskawitz’, and ‘Wonderful’) were microwave heated at 261 W for 102 s. Pomegranate seeds microwave pretreatment enhanced oil yield, yellowness index, total carotenoids content, total phenolic content, FRAP and DPPH radical scavenging capacity, despite an increase in conjugated dienes, and peroxide value. Palmitic acid, oleic acid, linoleic acid, saturated, and monosaturated fatty acids were increased after pomegranate seeds microwave pretreatment, whilst the levels of punicic acid and β-sitosterol were reduced. Nevertheless, the refractive index, the ratio of unsaturated to saturated fatty acid of the extracted oil were not significantly (p > 0.05) affected by pomegranate seeds microwave pretreatment. Principal component analysis and agglomerative hierarchical clustering established that ‘Acco’ and ‘Wonderful’ oil extracts from microwave pretreated PS exhibited better oil yield, whilst ‘Herskawitz’ oil extracts showed higher total carotenoids content, total phenolic content, and antioxidant capacity.