The utilization of beans (Phaseolus vulgaris L.) is hindered by unpleasant flavors, low macronutrients digestibility, and long cooking time. The pre-thermally treated beans can overcome these limitations. Therefore, the effect of thermal methods (moist–heat and dry-heat) and bean market classes (black, navy, kidney, and pinto) on functional properties and digestibility of bean flours were compared to raw counterparts. Within bean class, moist-heated samples showed increased water-holding capacities of 2.54–2.87 g H2O/g sample and starch/protein digestibility whereas dry-heated samples showed enhanced flavor profile and increased oil-holding capacities of 1.04–1.14 g oil/g sample. Among bean classes, moist-heated kidney bean flour showed the highest water-holding capacity of 2.87 g H2O/g sample and starch/protein digestibility while dry-heated pinto bean flour had the highest oil-holding capacity of 1.14 g oil/g sample. The current result may provide a basis for the development of pre-thermally treated legume flours and facilitate their applications.