Canola seeds were subjected to conventional and microwave heat treatments to investigate changes in the phenolic profile of defatted meal and oil obtained from the toasted seeds. Different temperature (120–200 °C) and time (5–20 min) combinations were applied for toasting the seeds in a conventional oven. The seeds were also toasted using a microwave oven at 300 Watt power level with and without steaming. Phenolics were extracted from the defatted meal and oil of raw and toasted seeds. The main phenolic compounds namely sinapine (SP), sinapoyl glucose (SG), sinapic acid (SA) and canolol were identified and quantified by HPLC-DAD. Total phenolics and SA derivatives in the meal were found to decrease in both toasting treatments. Canolol was formed in the oil and subsequently increased with increasing toasting temperature up to 200 °C. The optimum toasting conditions under which the canolol content of the oil showed the highest increment rate (more than 2200 folds) were found to be 200 °C for 15 min in the conventional oven. However, the optimum microwave toasting conditions were 20 min with steam which increased canolol content by more than 1700 folds.