Magnetite nanoparticles (MNPs) were synthesized using two distinctly different approaches, co-precipitation (CP) and thermal decomposition (TD), and further surface functionalized with organophosphonic ligands containing different numbers of phosphonic groups. We have shown that it is possible to fabricate flower-like assemblies of MNPs through TD at lower temperatures, whereas CP MNPs formed agglomerates of particles with broad size distribution and irregular shapes. The effect of the organophosphonic ligands on the heating efficiency of the TD and CP MNPs under dual mode stimulation (simultaneous action of AMF and NIR laser radiation) was studied for the first time. It was found that in the case of the cost-effective CP MNP synthesis surface functionalization with chosen phosphonic ligands leads to higher heating efficiency upon laser stimulation, whereas better performance of TD MNPs was found under the action of AMF due to the significant difference of nanoparticle properties. The biocompatibility of surface functionalized MNPs with organophosphonic ligands was evaluated through thorough studies of the metabolic activity of MNPs in normal human foreskin fibroblasts as well as oxidative stress induction and oxidation stress response which has not been previously reported for most of the organophosphonic moieties used in this study.