 In this study, a novel nanobiomaterial based on (3-aminopropyl)triethoxysilane (APTES)-coated iron oxide (Fe3O4) nanoparticles functionalized with newly synthesized guanine hydrazide (GH) was elaborated. A boron-doped diamond electrode coated with GH-APTES–Fe3O4 nanoparticles was used to assess the interaction of heavy metal ions with guanine hydrazide. The adsorption isotherms were electrochemically investigated and it was shown that the adsorption capacity of the nanoparticles towards heavy metals decreased in the following order: Cu2+ > Pb2+ > Cd2+. From the calibration curves, the sensitivities of detection were as follows: 171.6 µA/µM for Cu(II), 156 µA/µM for Pb(II), and 101.4 µA/µM for Cd(II).