The potential application of high capacity Sn-based electrode materials for energy storage, particularly in rechargeable batteries, has led to extensive research activities. In this scope, the development of an innovative synthesis route allowing to downsize particles to the nanoscale is of particular interest owing to the ability of such nanomaterial to better accommodate volume changes upon electrochemical reactions. Here, we report on the use of room temperature ionic liquid (i.e., [EMIm+][TFSI–]) as solvent, template, and stabilizer for Sn-based nanoparticles. In such a media, we observed, using Cryo-TEM, that pure Sn nanoparticles can be stabilized. Further washing steps are, however, mandatory to remove residual ionic liquid. It is shown that the washing steps are accompanied by the partial oxidation of the surface, leading to a core–shell structured Sn/SnOx composite. To understand the structural features of such a complex architecture, HRTEM, Mössbauer spectroscopy, and the pair distribution function were employed to reveal a crystallized β-Sn core and a SnO and SnO2 amorphous shell. The proportion of oxidized phases increases with the final washing step with water, which appeared necessary to remove not only salts but also the final surface impurities made of the cationic moieties of the ionic liquid. This work highlights the strong oxidation reactivity of Sn-based nanoparticles, which needs to be taken into account when evaluating their electrochemical properties.