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Trypsin inhibitor, a serine protease, is considered a major antinutritional factor in legumes. This naturally occurring protein is highly active over trypsin due to its stable structure, which depends mostly on its disulfide bonds. Several attempts have been carried out in order to inactivate trypsin inhibitor, being heat treatments the most effective ones. One of the problems when high temperatures are used is the reduction in the protein solubility, disabling legume isolates from being part of different food products. Herein a novel attempt for inactivation of trypsin inhibitor in soybean and chickpea is described where the use of L-cysteine is conceived to change the protein stability by altering it disulfide-bond integrity. Chickpea and soybean alkaline extracts were obtained from their respective defatted flours and over these extracts the effect of L-cysteine (3.6 mg/g sample) and thermal treatment (80º and 121ºC for soy and chickpea respectively) were tested. For soybean it was observed that trypsin inhibitor activity was mostly affected by thermal treatment (up to 76% of reduction) while the effect of L-cysteine was practically nonexistent (-1.88%). For chickpea counterpart, it was observed that treatment with 121°C was not effective in reducing trypsin inhibitor activity, being thus more resistant to high temperatures compared with the soybean counterpart.  On the other hand, the effect of L-cysteine on chickpea (at the same concentration mentioned above), significantly decreased its activity up to 60%. With this information differences in structure and activity of trypsin inhibitor from chickpea and soybean are devised but more tests will be required in order to fully understand dissimilarities. This information sets the possibility to develop new and selective strategies to reduce anti-nutritional activity according to legume source.