Azadirachta indica extract has been explored as an antibiotic in hygienic chitosan matrix system to enhance antimicrobial and medicinal property in a cost effective manner. The hygienic composite system has been successfully fabricated via solvent casting. The antibacterial activities of the hybrid system were examined by agar diffusion method against gram positive S.aureus and gram negative K. pneumoniae. From conventional antibacterial test for 24 h, the system exhibited an excellent antimicrobial activity against both bacterial strains in ranges of 1.2 cm -1.5 cm for S. aureus and 1.8 cm -2.3 cm for K. pneumoniae Fourier transform infrared spectroscopy revealed successfully embedded A. indica on the chitosan substrate via weak electrostatic interaction, resulting in the easy release of the additive. Moreover, atomic force microscopy showed a membrane roughness of 0.084 nm which confirms the uniform distribution of the additive throughout the membrane. These hybrid membranes have potential applications in skin tissue engineering, wound healing and as coatings for implantable scaffold material.