Nanotechnology for biomedicine has recently attracted increasing interest from the scientific community. In particular, among the different nanodevices suitable for this application, multifunctionalizable hybrid nanoparticles are one of the most investigated research topics. Here we present a detailed physico-chemical characterization of hybrid magneto-plasmonic iron oxide-gold nanoparticles (NPs) with core-shell structure. In particular, we underline all the synthetic difficulties concerning the preparation of these systems. Based on all our results, after different tests of a commonly reported protocol for the synthesis of the core-shell system, we believe that several issues are still open in the synthetic preparation of these particular NPs. Indeed, at least for the conditions that we adopted, core-shell morphology nanoparticles cannot be produced. However, independent of the core structure, we describe here an optimized and efficient functionalization protocol to obtain stable nanoparticle aqueous suspensions, which can be easily exported to other kinds of metal and metal-oxide NPs and used to develop biocompatible systems. Furthermore, reliable information that could be useful for researchers working in this field is extensively discussed.