Bentonite is naturally occurring material and can be considered as promising approach for targeting drug delivery. Special attention is paid to bentonite nanoparticles that are prepared by exfoliation technic from layered structure of bulk bentonite. The high surface area, adsorption capability, and biocompatibility make them excellent candidate for conjugation with antibacterial agents to diminish antimicrobial resistance. In this study, the prepared bentonite nanoparticles were non-covalently conjugated with the ciprofloxacin and then nanostructured ensemble bent@cip was studied as antibacterial delivery system with controlled release properties. The morphology and surface-charge modifications of synthesized bent@cip nanoensembles were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), zeta potential analyses; the loading and release kinetics were studied by ultraviolet–visible spectroscopy (UV–Vis) in physiological medium. The antibacterial activity of the prepared nanoensembles was evaluated against Gram-positive S. aureus and Gram-negative E. Coli bacterial strains using microbiological assays. Ciprofloxacin-loaded bentonite nanoparticles revel enhanced antibacterial activity compared with non-fictionalized bentonite, confirming the synergistic effect of the prepared nanoensemble.