The aim of our study was to develop a novel method for the preparation of polymeric core-shell nanoparticles loaded with various actives for biomedical applications. Poly(caprolactone) (PCL), poly(lactic acid) (PLA) and poly(lactide-co-glycolide) (PLGA) nanoparticles were prepared using the spontaneous emulsification solvent evaporation (SESE) method. The model active substance, Coumarin-6, was encapsulated into formed polymeric nanoparticles, then they were modified/functionalized by multilayer shells’ formation. Three types of multilayered shells were formed: two types of polyelectrolyte shell composed of biocompatible and biodegradable polyelectrolytes poly-L-lysine hydrobromide (PLL), fluorescently-labeled poly-L-lysine (PLL-ROD), poly-L-glutamic acid sodium salt (PGA) and pegylated-PGA (PGA-g-PEG), and hybrid shell composed of PLL, PGA, and SPIONs (superparamagnetic iron oxide nanoparticles) were used. Multilayer shells were constructed by the saturation technique of the layer-by-layer (LbL) method. Properties of our polymeric core-shell nanoparticle were optimized for bioimaging, passive and magnetic targeting.