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Abstract Low‐temperature synthesis in ionic liquids (ILs) offers an efficient route for the preparation of metal oxide nanomaterials with tailor‐made properties in a water‐free environment. In this work, we investigated the role of 1‐butyl‐1‐methylpyrrolidinium bis(trifluoromethylsulfonyl)imide [C4C1Pyr][NTf2] in the synthesis of cobalt oxide nanoparticles from the molecular precursor Co2(CO)8 with ozone. We performed a model study in ultra‐clean, ultrahigh vacuum (UHV) conditions by infrared reflection absorption spectroscopy (IRAS) using Au(111) as a substrate. Exposure of the pure precursor to ozone at low temperatures results in the oxidation of the first layers, leading to the formation of a disordered CoxOy passivation layer. Similar protection to ozone is also achieved by deposition of an IL layer onto a precursor film prior to ozone exposure. With increasing temperature, the IL gets permeable for ozone and a cobalt oxide film forms at the IL/precursor interface. We show that the interaction with the IL mediates the oxidation and leads to a more densely packed CoxOy film compared to a direct oxidation of the precursor.