Thermal treatment applied during the cooking of pulses leads to denaturation and even aggregation of the proteins, which may impact protein digestibility. Thermal transitions of lentil, chickpea, and bean proteins were studied using differential scanning calorimetry (DSC). Protein-enriched samples were obtained by dry air classification of dehulled seeds and were heated to 160 °C, with water contents ranging from 0.2 to 4 kg/kg on a dry basis. The DSC peaks of the resulting endotherms were successfully modeled as overlapping Gaussian functions. The denaturation temperatures were modeled as a function of the temperature according to the Flory–Huggins theory. The modeling allows for the calculation of the degree of protein transition for any temperature and moisture condition. The denaturation diagrams reflect the different protein compositions of lentil, chickpea, and bean (particularly the 11S/7S globulin ratio). Chickpea proteins were more thermally stable than those from lentil and bean. Proteins underwent an irreversible transition, suggesting that unfolding and aggregation were coupled.