The food industry is interested in the application of roasted flaxseeds because the treatment improves their sensory acceptability. However, it also influences flaxseed oil nutritional quality and stability. The aim of the study was to analyze oxidation changes in situ and in flaxseed oil compounds (fatty acids, phytosterols, tocochromanols) and Maillard reaction products (MRP) after roasting. The effect of the roasting temperature (160–220 °C) and flaxseed cultivars (golden‐ and brown‐seed) was taken into consideration. The results showed that the selection of roasting temperature (<200 °C vs. ≥200 °C) and flaxseed cultivar significantly influenced the nutritional quality and oxidative stability of roasted flaxseed oils. The roasting of flaxseeds did not significantly affect the fatty acid profiles of oil but it influenced the content of the other bioactive compounds. As the roasting temperature increased (≥200 °C), the γ‐tocopherol degradation decreased, whereas the content of plastochromanol‐8 increased. The total content of phytosterols in the roasted seed samples was higher than in the raw seeds but there was no correlation between the phytosterol content and roasting temperature. The temperature ≥200 °C significantly accelerated in situ oil oxidation during roasting. On the other hand, these conditions favored the MRP formation, which may have slowed down the dynamics of oil oxidation during storage. There was lower oil oxidation in the brown‐seed cultivar; in consequence, the tocopherol retention was higher than in the golden‐seed cultivars. The results could be useful for the selection of the best cultivars and treatment conditions to decrease unfavorable changes in flaxseed oil nutritional quality and stability.