Nanomedicine is entering a high maturity stage and is ready to reach full translation into the clinical practice. This is because of the ample spectrum of applications enabled by a large arsenal of nanostructured materials. In particular, bimetallic patchy core/shell nanoparticles offer tunable surfaces that allow multifunctional responses. Despite their attractiveness, major challenges regarding the environmental impact and biocompatibility of the obtained materials are yet to be solved. Here, we developed a green synthesis scheme to prepare highly biocompatible patchy core/shell magnetite/silver nanoparticles for biological and biomedical applications. The magnetite core was synthesized by the co-precipitation of ferric chloride and ferrous chloride in the presence of NaOH. This was followed by the patchy silver shell's growth by a green synthesis approach based on natural honey as a reducing agent. A purification process allowed selecting the target patchy nanoparticles and removing excess toxic reagents from the synthesis very efficiently. The obtained patchy magnetite/silver nanoparticles were characterized by UV-Vis spectrophotometry, dynamic light scattering (DLS), thermogravimetric analysis (TGA), Fourier transform infrared spectroscopy (FTIR), scanning electron microscope equipped with energy-dispersive spectroscopy (SEM + EDS), and transmission electron microscopy (TEM). The morphology, patchiness level, and size of the nanoparticles were determined via SEM and TEM. In addition, the spectrophotometric characterization confirmed the presence of the patchy silver coating on the surface of the magnetite core. The nanoparticles show high biocompatibility, as evidenced by low cytotoxicity, hemolytic effect, and platelet aggregation tendency. Our study also provides details for the conjugation of multiples chemistries on the surface of the patchy bimetallic nanoparticles, which might be useful for emerging applications in nanomedicine, where high biocompatibility is of the utmost importance.