This study was focused on the effect of microwave heating at different power (180, 360, 540, and 720 W) on phenolic compounds of methanol extracts of prickly pear seeds. The phenolic compositions of seeds showed a significant difference with roasting process compared with raw sample. The highest 1,2-dihydroxybenzene (77.94 mg/100 g), syringic acid (21.26) and caffeic acid (19.47 mg/100 g) contents were observed in seed sample roasted at 720 W, while the maximum trans-ferulic acid (16.89 mg/100 g) and quercetin (29.41 mg/100 g) amounts were determined in seed roasted at 360 W. Differences in phenolic compounds among different treatments were statistically significant (p <.05). In addition, syringic and trans-ferulic acid contents of prickly pear seed extracts gradually increased depending on microwave heating degrees compared with control group. The most suitable phenolic components of the prickly pear seeds heated in different microwaves were detected at 360 W. Generally, microwave roasting at 180 and 540 W decrease the contents of phenolics. Practical applications: Microwave heating has certain benefits such as speed, energy economy, process control precision and reduced start up and shut-down times. The food constituents depending on the characteristics of food product and other process variables can be affected by the microwave heating. In 16th century, prickly pear (Opuntia ficus-indica) was spreaded from American continent to South European countries. About 30–40% of prickly pear is composed of seeds. Seeds are rich in nutritive values such as polyphenols, flavonoids, minerals, fatty acids, tocopherols, tannins, glutamic acid, aspartic acid, leucine, lysine, and arginine as major amino acids. Prickly pear fruits are consumed freshly together with their seeds, and important for consumer health due to the phenolic constituents of seeds.