Inorganic nanoparticles (NPs) have emerged as promising tools in biomedical applications, owing to their inherent physicochemical properties and their ease of functionalization. In all potential applications, the surface functionalization strategy is a key step to ensure that NPs are able to overcome the barriers encountered in physiological media, while introducing specific reactive moieties to enable post-functionalization. Silanization appears as a versatile NP-coating strategy, due to the biocompatibility and stability of silica, thus justifying the need for robust and well controlled silanization protocols. Herein, we describe a procedure for the silica coating of harmonic metal oxide NPs (LiNbO3, LNO) using a water-in-oil microemulsion (W/O ME) approach. Through optimized ME conditions, the silanization of LNO NPs was achieved by the condensation of silica precursors (TEOS, APTES derivatives) on the oxide surface, resulting in the formation of coated NPs displaying carboxyl (LNO@COOH) or azide (LNO@N3) reactive moieties. LNO@COOH NPs were further conjugated to an unnatural azido-containing small peptide to obtain silica-coated LNO NPs (LNO@Talys), displaying both azide and carboxyl moieties, which are well suited for biomedical applications due to the orthogonality of their surface functional groups, their colloidal stability in aqueous medium, and their anti-fouling properties.