The number of antibiotics available to treat infectious diseases caused by multidrug-resistant organisms (MDROs) is often limited. These clinical issues show the urgent need for new antimicrobial solutions that are both safe and reliable. Nanotechnology discipline that is based on the development of nanostructures with improved antimicrobial efficacy against the deteriorating diseases proves to be an interdisciplinary approach as nanoparticles (NPs) exhibiting antibacterial properties may attack a variety of biomolecules, potentially reducing the evolution of MDROs by several resistance mechanisms. NPs synthesis by physical and chemical approaches is commonly believed to be the best for generating uniformly sized nanoparticles with long-term stabilization. These methods, however, are costly and result in introduction of hazardous chemicals into the atmosphere. This paper revealed the cost-effective and eco-friendly mode of NPs production. The fungus Shizophyllum commune has been used as a source of biological synthesis of silver nanoparticles (AgNPs) and copper nanoparticles (CuNPs) which may exhibit potential antimicrobial activity against various multidrug-resistant (MDR) microbes. The characterization was determined by ultraviolet-visible spectroscopy, dynamic light scattering, Fourier transform infrared spectroscopy and transmission electron microscopy. The NPs were found to be monodispersed and spherical shaped. The antimicrobial efficacy of these NPs was further checked by agar well diffusion method against MDR bacterial like Salmonella abony, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus. Thus, these biosynthesized NPs demonstrated a range of biomedical applications towards pathogenic microbes and bio-control of fungal strains, showing their potential to solve health-related problems in novel ways.