Protic ionic liquids are promising electrolytes for fuel cell applications. They would allow for an increase in operation temperatures to more than 100 °C, facilitating water and heat management and, thus, increasing overall efficiency. As ionic liquids consist of bulky charged molecules, the structure of the electric double layer significantly differs from that of aqueous electrolytes. In order to elucidate the nanoscale structure of the electrolyte–electrode interface, we employ atomic force spectroscopy, in conjunction with theoretical modeling using molecular dynamics. Investigations of the low-acidic protic ionic liquid diethylmethylammonium triflate, in contact with a platinum (100) single crystal, reveal a layered structure consisting of alternating anion and cation layers at the interface, as already described for aprotic ionic liquids. The structured double layer depends on the applied electrode potential and extends several nanometers into the liquid, whereby the stiffness decreases with increasing distance from the interface. The presence of water distorts the layering, which, in turn, significantly changes the system’s electrochemical performance. Our results indicate that for low-acidic ionic liquids, a careful adjustment of the water content is needed in order to enhance the proton transport to and from the catalytic electrode.