Response surface methodology was used to investigate the effects of extrusion conditions – namely moisture content (12.3–23.7 g 100 g−1) and temperature (150–178 °C) – on physicochemical, antinutritional compounds, functional and pasting properties of extruded bean cotyledons. Results indicated that extrusion cooking did not change the chemical composition of bean flours, but completely eliminated the activity of the trypsin and α-amylase inhibitors and haemagglutinins. The extrusion significantly improved starch and protein digestibility, water solubility and absorption of bean cotyledon. In addition, extrusion conditions significantly affected pasting properties, resulting in extrudate flours with different peaks and final viscosity values. From the results obtained in this work, it is possible to design a product with specific physicochemical, functional and nutritional properties using the appropriate moisture and temperature during extrusion.