Fruit seed is a by-product of fruit processing into juice and other products. Despite being treated as waste, fruit seed contains oil with health benefits comparable or even higher than the conventional seed oil from field crops. In addition to essential fatty acids, the fruit seed oil is a rich source of bioactive compounds such as tocopherols, carotenoids, flavonoids, phenolic acids and phytosterols, which have been implicated in the prevention of chronic and degenerative diseases such as cancer, diabetes and cardiovascular diseases. The emerging potential of fruit seed oil application in food and nutraceuticals has prompted researchers to study the effect of preharvest and processing factors on the seed oil quality with respect to nutritional qualities, antioxidant compounds and properties. Herein, the effect of cultivar, fruit-growing region, seeds pretreatment, seeds drying and seed oil extraction on tocopherols, polyphenols, phytosterols, carotenoids, fatty acids, antioxidant activity and oxidative stability of the fruit seed oil is critically discussed. Understanding the influence of these factors on seed oil bioactive phytochemicals, nutritional qualities and antioxidant properties is critical not only for genetically improving the oilseeds plants with desired characteristics, but also in seed oil processing and value addition. Therefore, preharvest and processing factors are essential considerations when determining the application of fruit seed oil.