The effect of heating (roasting and microwave radiation heating) along with a traditional pistachio flavouring mixture (containing verjuice, thyme extract, and sodium chloride) was investigated on reducing aflatoxins (AFs) and ochratoxin A (OTA) in pistachios. The naturally and artificially contaminated samples were soaked in the flavouring mixture (for 5, 10 and 24 h) and then subjected to roasting (at 120 and 150 °C for 50 min) and heating by microwave radiation (6 and 10 min). The residual mycotoxins were determined by high-performance liquid chromatography. The results showed that all treatments were able to reduce mycotoxin content (aflatoxin B1, B2, G1, G2 and OTA) significantly (P<0.05), up to 85.7±2.5% (during roasting) and up to 72.5±2.6% (during heating by microwave radiation). The highest reduction of AFs and OTA (ranging from 51.7±2.3 to 85.7±2.5%) was found when the contaminated (naturally and artificially) samples were soaked in the traditional mixture for 24 h and roasted at 150 °C. It could be concluded that the traditional flavouring method in combination with the roasting process or heating by microwave radiation could be applied as a useful and safe method for mycotoxin degradation in pistachio. Although, complete elimination of mycotoxins was not achieved, the method reduced mycotoxins more than 60% without adverse effect on the taste and appearance of pistachios.