The aim of the present study was to quantify some nutritional and safety quality parameter changes that take place in nuts (roasting) and sesame seeds (dehulling, roasting, milling, and sterilization) during processing. Such evaluation was based on chemical analysis of various indicators of lipid alteration in raw and processed pistachios, almonds, peanuts, and tahina. Lipid oxidation was assessed by the evolution of lipid oxidation products including hydroperoxides, p-anisidine, and thiobarbituric acid reactive substances, as well as carboxymethyllysine (CML) and trans fatty acids (tFAs). All these parameters were significantly affected by the different processing stages, especially by roasting and sterilization (tahina). Nut roasting and sesame heat treatment increased the primary (hydroperoxides) and secondary (aldehydic compounds) lipid oxidation products, with the p-anisidine value reaching 6-11.5 and thiobarbituric acid reactive substances 3-5 mg/kg (equiv of malondialdehyde) in the different end products. In addition, roasting led to the formation of CML (between 12.7 and 17.7 ng/mg) and tFAs (between 0.6 and 0.9 g/100 g) in nuts and tahina, which were absent in the raw material. Roasting parameters appear as the critical factor to control to limit the CML and tFA formation in the final product.