The combination of different nanomaterials through step-by-step synthesis procedures has turned into a promising alternative to fabricate high-quality nanosystems in order to satisfy the increasingly demanding requirements of the biomedical field. In this work, we report a detailed study on the synthesis and characterization of a complex nanosystem composed of nanoparticles with a single magnetic nanoparticle core and a shell of dense and mesoporous silica arranged in layers. The procedure designed to fabricate these systems lead us to the formation of a dispersion of non-agglomerated spherical nanoparticles of nearly 100 nm. The structural characterization performed over the final samples confirmed both the prevalence of single-core systems and the presence of the mesoporous silica shell in the outer layer. The performance of the nanosystem in a specific technological application was tested by sequentially loading two different fluorescents molecules by covalent and non-covalent bonding strategies. Due to the distinct loading strategies, the resulting nanosystem presented a magnetically-assisted probe & release functionality as analyzed in a magnetophoretic experiment.