Spherical magnetite nanoparticles (MNPs, 24 nm in diameter) were sequentially functionalized with trimethoxysilylpropyldiethylenetriamine (TMSPDT) and a synthetic DNA intercalator, namely, 9-chloro-4H-pyrido[4,3,2-kl]acridin-4-one (PyAcr), in order to promote DNA interaction. The designed synthetic pathway allowed control of the chemical grafting efficiency to access MNPs either partially or fully functionalized with the intercalator moiety. The newly prepared nanomaterials were characterized by a range of physicochemical techniques: FTIR, TEM, PXRD, and TGA. The data were consistent with a full surface coverage by immobilized silylpropyldiethylenetriamine (SPDT) molecules, which corresponds to 22300 SPDT molecules per MNP and a subsequent (4740 − 2940) PyAcr after the chemical grafting step (i.e., 2.4 PyAcr/nm2). A greater amount of PyAcr (30600) was immobilized by the alternative strategy of binding a fully prefunctionalized shell to the MNPs with up to 16.1 PyAcr/nm2. We found that the extent of PyAcr functionalization strongly affects the resulting properties and, particularly, the colloidal stability as well as the surface charge estimated by ζ-potential measurement. The intercalator grafting generates a negative charge contribution which counterbalances the positive charge of the single SPDT shell. The DNA binding capability was measured by titration assay and increases from 15 to 21.5 μg of DNA per mg of MNPs after PyAcr grafting (14−20% yield) but then drops to only 2 μg for the fully functionalized MNPs. This highlights that even if the size of the MNPs is obviously a determining factor to promote surface DNA interaction, it is not the only limiting parameter, as the mode of binding and the interfacial charge density are essential to improve loading capability.