Biocompatibility is a major concern for promising multifunctional bioactive materials. Unfortunately, bioactive materials lack biocompatibility in some respects, so active ingredient formulations are urgently needed. Bimetallic nanoparticles have demonstrated drawbacks in stabilized biocompatible formulations. This study examined the preparation of biomaterial-based multifunctional biopolymers via an eco-friendly formulation method using ultrasound. Bimetallic zinc oxide/iron oxide (magnetic form) nanoparticles (ZnO@Fe3O4NPs) were formulated using casein and starch as capping agents and stabilizers. The formulated nanocomposite was characterized using ultraviolet–visible spectroscopy (UV-vis), Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermal gravimetric analysis (TGA), scanning electron microscopy (SEM), and high-resolution transmission electron microscopy (HR-TEM). Herein, the formulated nanocomposite was shown to have a thermally stable nanostructure, and the bimetallic ZnO@Fe3O4 NPs were measured as 85 nm length and 13 nm width. Additionally, the biocompatibility test showed its excellent cytocompatibility with Wi 38 and Vero normal cell lines, with IC50 550 and 650 mg/mL, respectively. Moreover, the antimicrobial activity was noted against six pathogens that are represent to the most common pathogenic microbes, with the time required for killing of bacteria and unicellular fungi being 19 h and 61 h for filamentous fungi with remarket an excellent antioxidant activity.