Carbon nanotubes represent one of the best examples of novel nanostructures, exhibit a range of extraordinary physical properties, strong antimicrobial activity and can pierce bacterial cell walls. This investigation handles the antimicrobial activity of functionalised multiwall carbon nanotubes (F-MWNTs) as an alternative antimicrobial material compared to the commercial antibiotics. Antibacterial activities of F-MWNTs are investigated through two different kinds of bacteria, E. coli and S. aureus. The results demonstrate that the best concentration of F-MWNTs for the maximum inhibition and antibacterial functionality is 80 and 60 μg/ml for E. coli and S. aureus, respectively. The transmission electron microscope reveals the morphological changes damage mechanism for the cellular reliability on these microorganisms. F-MWNTs are capable of biologically isolating the cell from their microenvironment, contributing to the development of toxic substances and placing the cell under oxidative stress leading to cellular death. The efficiency of F-MWNTs is compared with the common antibiotics and shows an enhancement in the inhibitory effect with percentages reaches 85%. To account for the bactericidal performance of F-MWNTs towards these pathogens, the dielectric conductivity and the bacterial growth measurements are conducted. The present study endeavour that F-MWNTs could be exploited in biomedical devices and altering systems for hospital and industrial cleaning applications.