In this paper the results concerning the synthesis of magnetite (Fe3O4) nanoparticles (NPs), their functionalization using silane derivatives, such as (3-Aminopropyl)triethoxysilane (APTES) and (3-mercaptopropyl)trimethoxysilane (MPTMS), and their exhaustive morphological and physical characterization by field emission scanning electron microscopy (FE-SEM) with energy dispersion X-ray spectrometer (EDX) analysis, AC magnetic susceptibility, UV-VIS and IR spectroscopy, and thermogravimetric (TGA) analyses are reported. Two different paths were adopted to achieve the desired functionalization: (1) the direct reaction between the functionalized organo-silane molecule and the surface of the magnetite nanoparticle; and (2) the use of an intermediate silica coating. Finally, the occurrence of both the functionalization with amino and thiol groups has been demonstrated by the reaction with ninhydrin and the capture of Au NPs, respectively.