Anisotropic magnetic nanoparticles are receiving growing interest for biomedical applications due to their interesting properties, particularly for MRI and magnetic hyperthermia. In this work, a two-step, relatively simple synthesis pathway of magnetite nanorods was optimised. A ligand from the catechol family, known for its high iron oxide surface affinity, was used to transfer them into aqueous phase. The magnetite nanorods were then coated with a layer of fluorescent silica, whose surface was functionalised in two ways: either by short poly(ethylene glycol) (PEG) chains or by sulfobetaine zwitterionic molecules. A wide range of techniques were used to thoroughly characterise their physical structure, magnetic properties and dispersion characteristics. Finally, a study of the adsorption of a fluorescent model protein revealed that zwitterionic sulfobetaine molecules were more effective than PEG chains in limiting the non-specific adsorption of this protein.