Effect of several physical treatments (soaking, dehulling, ordinary cooking, microwave cooking, and autoclaving) on the level of antinutrients and in vitro protein digestibility of bitter and sweet lupin seeds were investigated. The raw bitter and sweet lupin seeds were found to contain phytic acid, tannins, trypsin inhibitor activity, and lectin activity, but $alpha$-amylase inhibitor was absent. Dehulling significantly increased the levels of phytic acid (PA), trypsin inhibitor activity (TIA), and tannins, but lectin activity was not changed. Also soaking in bitter (for 96 hr) and sweet (for 24 hr) seeds caused a significant increase in these factors except lectin activity. Cooking methods differently affected the levels of the antinutrients. Thus, PA increased but tannins were not changed, on the other hand TI and lectin activities were inactivated; ordinary cooking and autoclaving were the most effective in both seeds. For combination effect, soaking following cooking treatments significantly decreased PA, tannins, and lectin activity, but increased TIA in both seeds. Moreover, dehulling following soaking and cooking methods resulted in a significant increase of PA, TIA, and tannins. In vitro protein digestibility (IVPD) of raw bitter and sweet lupin seeds were 78.55 and 79.46%, respectively and it was improved by all processing methods; soaking-dehulling after autoclaving was the most effective in both seeds. Although some treatments increased the level of antinutrients, they improved IVPD. Therefore, the studied antinutrients are not the only responsible factor for lowering IVPD.