The electrocatalytical process at the air cathode in novel silicon–air batteries using the room-temperature ionic liquid hydrophilic 1-ethyl-3-methylimidazolium oligofluorohydrogenate [EMI⋅2.3 HF⋅F] as electrolyte and highly doped silicon wafers as anodes is investigated by electrochemical means, X-ray photoelectron spectroscopy (XPS), and electron paramagnetic resonance (EPR) spectroscopy. The results obtained by XPS and EPR provide a model to describe the limited discharge capacity by means of a mechanism of air-electrode deactivation. In that respect, upon discharge the silicon-air battery′s cathode is not only blocked by silicon oxide reduction products, but also experiences a major modification in the MnO2 catalyst nature. The proposed modification of the MnO2 catalyst by means of a MnF2 surface layer greatly impacts the Si–air performance and describes a mechanism relevant for other metal–air batteries, such as the lithium–air. Moreover, the ability for this deactivation layer to form is greatly impacted by water in the electrolyte.