The effect of heat treatments (boiling, autoclaving, microwave cooking and roasting) on the levels of certain antinutritional factors (phytic acid, trypsin inhibitor, α-amylase inhibitor, lectin activity and tannins) and in vitro protein digestibility (IVPD) of peanut and sesame seeds were investigated. All heat treatments significantly reduced the levels of all the investigated antinutrients and improved the IVPD of peanut seeds. Of the attempted treatments, autoclaving, boiling, roasting-salting and oil-roasting were the most effective in reducing the levels of antinutrients and improving IVPD of peanut. Roasting in both brown and white sesame seeds partially eliminated the studied antinutrients (the reduction ranged from 15.6% to 61.2% in all antinutrients) and improved IVPD (increased by 10% and 9.1%, respectively). Also, Tehineh (sesame butter-like) contained lower levels of antinutrients than raw sesame seeds and exhibited a higher IVPD (82.8%).