We investigated proton-induced transmittance modulation in amorphous WO3.2 films with methods of analysis including variable angle spectroscopic ellipsometry (VASE) and atomic force microscopy (AFM). We induced optical transition from the clear to the colored state by injecting electrons and protons into the WO3.2 film. A decrease in the index of refraction, accompanied by an associated increase in the extinction coefficient in the visible range of the spectrum was measured with VASE upon the transition. Physical modulation in terms of a change in the surface morphology was characterized. AFM measurements showed enlargement of a characteristic domed surface structure as the transition took place from the clear to the colored state without significant change in the rms surface roughness value.