Recently, graphene-based nanocomposites are increasingly becoming popular for a variety of biological applications, due to their extraordinary physicochemical properties. Herein, we present an eco-friendly method for the preparation of a novel nanocomposite based on reduced graphene oxide (rGO) decorated with tin oxide (SnO2) and zinc oxide (ZnO) nanoparticles. The rGO and binary metal oxides-based nanocomposite (rGO/ZnO/SnO2) with enhanced biocompatibility was prepared by using Mentha longifolia extract as a non-hazardous reducing agent. The rich polyphenolic and flavonoids contents of Mentha longifolia have functioned as potential bio-reductants, which are not only suitable for the synthesis of rGO/ZnO/SnO2, but also effectively stabilized the resulting composite. Initially, to determine the reducing ability of Mentha longifolia, the redox potential and chemical composition of green extract was investigated by cyclic voltammetry (CV) and liquid chromatography-mass spectrometry (LC-MS), respectively. On the other hand, the structural composition and morphology of the resultant composite was confirmed by X-ray diffraction (XRD), Raman spectroscopy, Fourier transform infrared spectroscopy (FT-IR) and UV–visible spectroscopy (UV), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDS). Furthermore, the biological potential of rGO/ZnO/SnO2 is determined by evaluating the antimicrobial and antifungal properties of the resulting composite against various pathogens such as, Staphylococcus aureus (SA), Candida albicans (CA) and Clostridium dificile (CD). Notably, the composite has demonstrated superior antibacterial and antifungal properties when compared to its individual counterparts including rGO, SnO2 and ZnO. Density functional calculations complement the experimental findings, as the periodic boundary conditions reveal high binding energy of −14.8 keV for the rGO/ZnO/SnO2 nanocomposite.