Electrochemical Impedance Spectroscopy (EIS) was employed to estimate the global transverse proton diffusion coefficient, DH+, in sulfonic acid functionalized sustainable chitosan (CS-SO3H)/Nafion composite films. In contrast to conventional conductivity measurements, EIS measurements were performed at room temperature with a film/liquid interface. In this configuration, the measure of the bulk proton transport is correlated to the DH+ of the membranes which is close to 1.1 × 10−6 cm2 s−1 and 0.33 × 10−6 cm2 s−1 with and without CS-SO3H, respectively. These DH+ values permitted the proton conductivity (σH+) ratio (∼3.9) between the Nafion/CS-SO3H composite and pristine Nafion films to be estimated by using the Nernst-Einstein relationship. This ratio presents a good agreement with that obtained for the σH+ of bulk membranes (∼3.2) measured at 30 °C and 90% RH. The agreement between the σH+ ratios validates our methodology for DH+ estimation by EIS and suggests that the more than three times enhanced σ+HσH+ is governed by the ∼3 times higher DH+ in the presence of CS-SO3H.