Selected legume seeds (dry and soaked) including faba beans, peas, chickpeas, soybeans, lentils and common beans containing 8 and 25% moisture, respectively, were subjected to microwave heating, and to a conventional cooking method to determine the heating effect on toxic compounds and protein quality. Trypsin inhibitors, hemagglutinins and available lysine were analyzed, and laboratory rats were used to determine digestibility and protein efficiency ratio (PER). Results indicated that microwaving destroyed trypsin inhibitors to a similar degree to that observed in beans cooked using the conventional method without affecting PER for raw seeds with low antinutrients content (faba beans, peas, chickpeas and lentils). Microwave-heated soaked soybeans had a higher amount of destroyed trypsin inhibitors, along with a higher PER, compared with microwave-heated dry soybeans. Microwave heating of common beans failed to destroy hemagglutinins and trypsin inhibitors, and consequently their digestibility and PER values were poor. Finally it was concluded that microwave heating constitutes an adequate method for destroying hemagglutinins and trypsin inhibitors without affecting protein quality of most legume seeds, except for common beans that despite of this process retained the antinutritional substances.