Iron (Fe)-based nanoparticles are extremely valuable in biomedical applications owing to their low toxicity and high magnetization values at room temperature. In this study, we synthesized nearly monodisperse iron oxide (Fe3O4) and Fe@Fe3O4 (core: Fe, shell: Fe3O4)4) nanoparticles in aqueous medium under argon flow and then, coated them with various biocompatible ligands and silica. In this study, eight types of surface-modified nanoparticles were investigated, namely, Fe3O4@PAA (PAA = polyacrylic acid; MwMw of PAA = 5100 amu and 15,000 amu), Fe3O4@PAA–FA (FA = folic acid; MwMw of PAA = 5100 amu and 15,000 amu), Fe3O4@PEI–fluorescein (PEI = polyethylenimine; MwMw of PEI = 1300 amu), Fe@Fe3O4@PEI (MwMw of PEI = 10,000 amu), Fe3O4@SiO2 and Fe@Fe3O4@SiO2 nanoparticles. We characterized the prepared surface-modified nanoparticles using high-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), Fourier transform infrared (FT-IR) absorption spectroscopy, a superconducting quantum interference device (SQUID), X-ray photoelectron spectroscopy (XPS), photoluminescence (PL) spectroscopy and confocal microscopy. Finally, we measured the cytotoxicity of the samples. The results indicate that the surface-modified nanoparticles are biocompatible and are potential candidates for various biomedical applications.