The stability of deoxynivalenol (DON), deoxynivalenol-3-glucoside (DON-3-glucoside), 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON), de-epoxy-deoxynivalenol (DOM-1) and ochratoxin A (OTA) during thermal processing has been studied. Baking temperature, time and initial mycotoxin concentration in the raw materials were assayed as factors. An improved UPLC-MS/MS method to detect DON, DON-3-glucoside, 3-ADON, 15-ADON and DOM-1 in wheat baked products was developed in the present assay. The results highlighted the importance of temperature and time in mycotoxin stability in heat treatments. OTA is more stable than DON in a baking treatment. Interestingly, the DON-3-glucoside concentrations increased (>300%) under mild baking conditions. On the other hand, it was rapidly reduced under harsh conditions. The 3-ADON decreased during the heat treatment; while DOM-1 increased after the heating process. Finally, the data followed first order kinetics for analysed mycotoxins and thermal constant rates (k) were calculated. This parameter can be a useful tool for prediction of mycotoxin levels.