Oxidative polymerization of aniline in the presence of Nafion membranes has been carried out in a water–isopropanol mixture after preliminary impregnation of the membrane with the monomer (aniline) in aqueous isopropanol. Uniform distribution of polyaniline (PANI) throughout whole membrane volume has been found. On the contrary, aniline polymerization in water, even after preliminary impregnation of the membrane with the monomer, has resulted in the formation of PANI thin layer only on the membrane surfaces but not inside the membrane. The polymerization in water–isopropanol mixture has not led to the change in the membrane surface properties but has induced the structural reorganization of Nafion membrane accompanied by the increase in the membrane ionic cluster size and the distance between the fluorocarbon crystallites. Modification by PANI carried out either in water or in aqueous isopropanol solution has resulted in the decrease in the membrane proton conductivity by 5–10 times.