In this study, the effects of different microwave powers on the bioactive properties, fatty acid and phenolic profiles of pomegranate seed oil were reported using various analytical methods, GC and HPLC. Antioxidant capacity and total phenolic values of pomegranate seed oils were established between 14.16% (control) and 19.18% (720 and 900 W) to 0.00 (900 W) and 3.61 mgGAE/100 g (control), respectively. The viscosity values of pomegranate seed oil increased with the heat treatment. But, the viscosity of the oils increased with the applied Watt increase. The p-coumaric acid amounts of the seed oils heated at 180, 720 and 900 W in the microwave were found to be statistically similar. In general, phenolic compounds of pomegranate seed oils did not show a constant increase or decrease depending on microwave power. The key fatty acid of pomegranate seed oil was punisic acid (30.49–36.10%). followed by linoleic acid (25.95–30.01%).