The present study was conducted to determine the composition of pomegranate seed oils according to fruit cracking and maturity stage. Quality attributes and fatty acid profile of seed oils of intact and cracked fruits from two pomegranate varieties (Gabsi and Chelfi) were studied at two different harvest dates (1 September and mid October). The variety, harvest date, and fruit cracking were proved to affect significantly seed oil quality. Gabsi’ variety exhibited higher seed oil content and total phenolic content compared to those in ‘Chelfi’ fruits. However, seed oils from ‘Chelfi’ fruits were characterized by the highest amounts of palmitic, palmitoleic, linoleic, and stearic acids. Seeds from cracked fruits exhibited higher oil content than those in intact fruits. Fruit cracking increased the peroxide value, phenol concentration, and the contents of linoleic, linolenic, catalpic, and erucic acids while decreased the β-carotene content. Changes occur in analytical parameters and fatty acid profile as the ripening process progressed. A significant decrease in free acidity content was noted while the peroxide value, the palmitic and linoleic acid contents increased with the delay of harvest. Therefore, the variety, fruit cracking, and harvest date contribute largely to the characteristics of pomegranate seed oils.