Surface and bulk chemical changes in a Nafion membrane as a result of room temperature ionic liquids (RTILs) incorporation were determined by X-ray photoelectron spectroscopy (XPS) and elemental analysis, respectively. RTILs with different physicochemical properties were selected. Two imidazolium based RTIL-cations (1-octyl-3-methylimidazolium and 1-butyl-3-methylimidazolium) were used to detect the effect of cation size on membrane modification, while the effect of the RTIL hydrophilic/hydrophobic character was also considered by choosing different anions. Angle resolved XPS measurements (ARXPS) were carried out varying the angle of analysis between 15° and 75° to get elemental information on the Nafion/RTIL-modified membranes interactions for a deepness of around 10 nm. Moreover, changes in the RTIL-modified membranes associated to thermal effect were also considered by analyzing the samples after their heating at 120 °C for 24 h. Agreement between both chemical techniques, bulk and destructive elemental analysis and surface and non-destructive XPS, were obtained.