The herbal-based drug isolation-related research has increased recently around the globe. Accordingly, the current study was designed to evaluate the phytochemical content of ethanol extract of Martynia annua and its chitosan nanoparticles (MA-CNPs) antibacterial activity against bacterial pathogens such as Bacteroides fragilis, Streptococcus oralis MTCC 2696, Propionibacterium acnes MTCC 1951, Pseudomonas aeruginosa MTCC 424, Staphylococcus aureus MTCC 2940, E. coli MTCC 443, Bacillus cereus MTCC 441, Streptococcus mutans MTCC 890, Aeromonas hydrophila MTCC 12301, and Streptococcus faecalis by agar well diffusion methods. The obtained results showed that the ethanol extract of M. annua contains more pharmaceutically valuable phytochemicals than other solvent extracts and its mediated chitosan nanoparticles showed effective antibacterial activities. The ethanol extract also effectively reduced, capped, and stabilized the chitosan into MA-CNPs. The green synthesized MA-CNPs were characterized and confirmed through UV-visible spectrophotometer, FT-IR, SEM, and DLS analyses. The MA-CNPs exhibited considerable antibacterial activity in the order of Bacteroides fragilis > Streptococcus oralis > Propionibacterium acnes > Pseudomonas aeruginosa > Staphylococcus aureus > E. coli > Bacillus cereus > Streptococcus mutans > Aeromonas hydrophila> Streptococcus faecalis. Finally, the results strongly recommended that the ethanol extract of M. annua-mediated chitosan nanoparticles could be considered an effective nanomaterial to control microbial pathogens. Further, therapeutical uses of MA-CNPs need in vitro and in vivo investigation.