This work reports the magnetite-functionalization and biological evaluation of eugenol by the co-precipitation method employed only Fe2+ under mild conditions and control from the amount of the incorporated magnetite. Magnetic nanoparticles were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared (FTIR), hydrodynamic size distribution (Zetasizer), and vibrating sample magnetometer (VSM). SEM images showed that EUG·Fe3O4 similar in shape to a nanoflower. The FTIR spectrum confirmed the presence of characteristic EUG and Fe3O4 bands in the EUG·Fe3O4 sample, the XRD analysis showed that the magnetite functionalization with eugenol slightly affected the Fe3O4 crystal structure, while the VSM measurements demonstrate that EUG·Fe3O4 1:1 shows a superparamagnetic behavior, suggesting small non-interacting particles. The in vitro safety profile and cytotoxicity of free eugenol, magnetite pristine, EUG·Fe3O4 1:1, EUG·Fe3O4 1:5, and EUG·Fe3O4 1:10 was investigated using human cell lines (keratinocytes and melanoma). The results demonstrate the high biocompatibility of EUG·Fe3O4 in HaCat cells and the greater specificity for the A375 cell line. Furthermore, the magnetite-functionalization with eugenol decreased the toxic effects of free eugenol on healthy cells. Antibacterial tests were performed in different bacterial strains. The experimental data showed that among the magnetic compounds, the microorganisms were only sensitive to treatment with EUG·Fe3O4 1:1. Regarding the antibiofilm activity assay, it can be observed that only the EUG·Fe3O4 caused a significant decrease in biomass when compared to the positive control. Finally, it can be concluded that EUG·Fe3O4 proves to be a potential candidate for future studies for drug delivery of cancer and bacterial infections treatments.