Biocompatible and non-toxic properties of chitosan make it a candidate with excellent application prospects in developing wound dressing conjugate compounds. Six different chitosan-based nanohybrid membranes were evaluated against multi-drug resistant bacterial isolates. Twenty-seven drug-resistant Staphylococcus aureus, Enterococcus faecalis, Acinetobacter baumannii, and Pseudomonas aeruginosa species were isolated from burn wound infections. Different combinations of chitosan, ciprofloxacin (CIP), biofunctionalized montmorillonite (MMT), and montmorillonite with sulfate chains (SMMT) were provided, and their antibacterial activity was assessed using the colony count method. Six Methicillin-resistant S. aureus, seven vancomycin-resistant E. faecalis, four A. baumannii, and 10 P. aeruginosa multi-drug resistant were identified. Chitosan and montmorillonite did not show significant antibacterial effect but, chitosan/SMMT/CIP was the most effective nanocomposite. Chitosan-based nanocomposites with ciprofloxacin could effectively reduce the susceptibility of drug-resistant bacterial isolates. Bacterial targeting using nanosystems provides an opportunity for effective antibiotic treatment by improving antibacterial efficacy.