The advent of multidrug-resistant microorganisms and associated outbreaks are major threats facing humanity. Therefore, additonal approaches are being explored, so as to create new antimicrobial agents that can be utilized over multiple cycles. To this end, functionalized clay with metal nanoparticles for antimicrobial applications has been formulated. Natural Kalzhat clay from the Almaty region of Kazakhstan was functionalized with silver and copper nanoparticles, following their in-situ synthesis. The unprocessed Kalzhat clay was characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR), and elemental analysis (EDX). The clay was treated with sodium carbonate before functionalization. The EDX, FT-IR and XRD analysis of the clay confirmed the presence of bentonites. The synthesized nanoparticles of silver and copper were also characterized using transmission electron microscopy (TEM), FT-IR, and EDX analysis. TEM images of the nanoparticles confirmed a spherical morphology in the nano size range, with an average diameter of 29.85±14.34nm for AgNPs and of 75.37±28.24 nm for CuNPs. The clay impregnated with Ag and Cu nanostructures showed excellent antimicrobial activity against pathogenic gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli) bacteria, with inhibition zones of 10.5mm (AgNP) and 25mm (CuNP), and of 8.5mm (AgNP) and 13.5mm (CuNP), respectively. Hence, such metal nanoparticles incorporated into clay show promising anti-bacterial application, suggesting that clay could be used as a functional material in order to limit the spread of bacteria in agricultural and biomedical applications.