Core-shell magnetic nanoparticles (MNPs) offer tremendous opportunities in a large range of applications in biomedicine due to their superior magnetic properties, biocompatibility and suitability for modification. In most cases, these characteristic features are determined by their shell chemistry and morphology. Herein, we demonstrate a comparative study of silica and polydopamine (PDOP) coating onto MNP surfaces based on synthesis, characterization and usage in a bio-separation platform. It was found that monodispersed MNPs may be easily obtained on silica coating of varying shell thickness, whereas a continuous PDOP layer observed around the MNPs prevents the formation of the dispersed form. On the other hand, PDOP coated MNPs exhibited better superparamagnetic behavior and biological modification ability compared to the silica coated form.