FePt-Fe3O4 core-shell nanoparticles functionalized with 3,4-dihydroxyphenylacetic acid (DOPAC) and dimercaptosuccinic acid (DMSA) ligands were synthesized and characterized. We found that the DOPAC ligand enhances the magnetic properties of the FePt-Fe3O4 particles, in comparison with the DMSA ligand, which induces the oxidation of the shell layer that causes a significant reduction of the saturation magnetization. The synthesized magnetic nanoparticles were evaluated for applications in magnetic hyperthermia and magnetic resonance imaging contrast enhancement.