Fe3O4 nanoparticles were prepared by a very promising bottom-up chemical strategy and covered by a biocompatible fluorescent silica coating by an improved microemulsion method. An accurate analysis of some key process parameters, to obtain a controlled nanoparticles covering, has been performed. The co-encapsulation of Fe3O4 nanoparticles and large amount of FITC dye molecules together, via silica shell (preventing the fluorescence quenching of the nanoprobes), and the grafting of primary amines (very active functional groups) into the silica surface, have been obtained. Moreover, the as-synthesized nanoprobes can be well-dispersed in aqueous solution.