This study was conducted to investigate the impacts of microwave heating treatments at different powers (0, 180, 360, 540, 720 and 900Watts) on the quality attributes of chia seed oil. Linoleic acid contents of the chia seed oil heated in microwave oven changed between 19.21% (900 W) and 21.17% (control), respectively (p < 0.05). Linolenic acid contents of heated chia seed oils varied between 66.84% (900 W) and 68.71% (control). α-Tocopherol and β-tocopherol contents of the chia oil samples varied between 47.71 mg/100 g (900 W) and 51.17 mg/100 g (control) to 62.58 mg/100 g (900 W) and 67.81 mg/100 g (control), respectively. While caffeic acid contents of the oils change between 0.27 mg/g (900 W) and 3.84 mg/g (control), rosmarinic acid contents of chia seed oils were found between 1.32 mg/g (900 W) and 3.17 mg/g (control). Results reflect a change in the chemical structures of the chia oil. Overall, much care should be taken when roasting chia seeds in microwave to avoid lossess in the bioactive components of chia oil.