Various metal (Ag, Au, and Pt)@thiol-functionalized silica (SiO2-SH) nanoparticles (NPs) are successfully prepared at room temperature by a facile, efficient, functional, universal and scalable coating process in alcohol-free aqueous solution using pre-hydrolyzed 3-(mercaptopropyl)trimethoxysilane (MPTMS). The controlled pre-hydrolysis of the silane precursor in water and the consecutive condensation processes are the key to achieve the effective and uniform silica coating on metal NPs in aqueous solution. The thickness of the silica shell is tuned by simply varying the coating time. The silica shell can act as an effective protecting layer for Ag NPs in Ag@SiO2-SH NPs under conditions for silica coating in aqueous solution; however, it leads to a directional dissolution of Ag NPs in a more strongly basic ammonia solution. The environmentally friendly silica coating process in water is also applied to prepare highly surface-enhanced Raman scattering (SERS)-active Ag@SiO2-SH NPs with different types of Raman molecules for highly sensitive SERS-based applications in various fields.