Extrusion processing has been used to modify the functional properties of proteins. The protein-protein interactions, surface hydrophobicity, and rheological properties of milk protein concentrate extruded using dies of different geometries (circular, annular and slit) were quantified. With the same extrusion treatment history prior to the die, extrudates generated using dies with higher wall shear (slit 1.4 × 104 s−1 > annular 1.1 × 104 s−1 > circular 2.9 × 103 s−1) showed greater protein extractability, higher index of surface hydrophobicity, and enhanced water solubility index indicating significant breakdown of protein aggregates. Higher viscoelastic moduli (G' and G") and apparent viscosity were observed for slit die extrudate dispersions. However, low flow behavior indices (0.04–0.23(−)) and a high viscous activation energy (43 kJ/mol) of slit die extrudate dispersions implied their shear and temperature sensitivity, respectively. Thus, extrudate functionality can be optimized by selection of the appropriate die design.