This paper describes the use of methoxy-poly(ethylene glycol) silane (MPEG-sil) as a linker molecule for the synthesis of silica-coated nanoparticles by the Stöber method. While short alkane chain-based siloxanes including (acryloxypropyl)trimethoxysilane and 3-methacryloxypropyl-trimethoxysilane are popular molecules used in surface modification, they are not efficient for the silica coating of nanoparticles synthesized from organic solvents containing long carbon chain carboxylic acids or amines as capping agents. Here, we report the utilization of MPEG-sil to bridge this gap. Our approach is based on a two-phase system, in which ligand exchange takes place in a hydrophobic environment and the surface modification with silica is conducted in an ethanol-water mixture. Our results show that this two-phased approach was effective to coat monodisperse Fe2O3 nanoparticles capped with oleic acid and Ag nanoparticles capped with oleylamine with uniform SiO2 shells. The process was also demonstrated for double-shell nanostructures to produce SiO2-coated Pt@Fe2O3 core-shell nanoparticles. The results described in this work represent a new approach for the surface modification with silica coating of monodisperse nanoparticles synthesized from nonhydrolytic solutions and can potentially have a broad ramification in the development of water-dispersible nanoparticles for biological applications.