Legumes are high in protein but also contain heat labile trypsin inhibitors (TI’s) that reduce protein digestibility. To test if cooking at high altitudes is less effective at inactivating TI than cooking at sea level, common beans and fava beans were cooked in water at temperatures chosen to simulate boiling points at different altitudes. In addition, each variety was autoclaved in water at 121°C to simulate a pressure cooker. Trypsin inhibitor activity (TIA) was measured with N-α-Benzoyl-L-arginine 4-nitroanilide hydrochloride, and in vitro protein digestibility was determined by digestion of samples with 3 peptidases. Raw common and raw fava beans inhibited 100% and 36% of trypsin activity, respectively. Cooking common beans at 100°C inactivated 88.6% (SD±4.8) of TI, while cooking at temperatures between 87-97°C inactivated 73.2% (p<0.05). In fava beans, TI inactivation was 75% at all cooking temperatures. TI inactivation in an autoclave was positively correlated with time for common beans (p<0.05) but not fava beans. Protein digestibility in common beans was 79.1% in raw beans, 85.0% in beans cooked at 87°C and 89.7% in beans cooked at 100°C. Fava bean digestibility was greater than that of common beans when raw (86.0%) and when cooked at 100°C (95.6%). Regression analysis showed a negative correlation between TIA and protein digestibility (r2=0.86). Residual TIA of common beans cooked at high altitudes in boiling water is higher than when cooked at sea level, lowering protein digestibility. In populations where protein intakes are marginal, this could negatively impact protein nutritional status.