•This study aims to evaluate the contribution of chitosan nanoparticles to enhance the antimicrobial activity.•Nisin and Natamycin will be applied either in the free-state or loaded on chitosan nanoparticles.•Disc diffusion assay, Lb. helveticus crude CFS recorded the highest potency against all bacterial indicators.•The recorded MIC values were found to be higher in case of tested bacteria than yeast and fungus.•CFS with HS–GC–MS showed that Lb. helveticus produces a wide range of antimicrobial& health-promoting substances. This research attempted to inspect the contribution of lactic acid bacteria (LAB) with nanoparticle application in antimicrobial enhancement. Seven lactic acid cultures-free supernatants (CFSs) in both free and nanoparticles-loaded states were examined against seven foodborne microorganisms. Lactobacillus helveticus followed by Lactobacillus Plantarum possessed considerable antimicrobial activity. Headspace GC–MS characterization of Lactobacillus helveticus CFS identified a mixture of antimicrobial and health-promoting compounds. Minimal inhibitory concentration (MIC) values for tested Gram-positive bacteria represented 50% of that for Gram-negative bacteria, 20% and 7.35% of those for fungus and yeast respectively. Nanoparticles were prepared through chitosan-tripolyphosphate nanoparticle formation giving nanospheres from in the range from 5 to 10 nm, and narrow size distribution. CFS-loaded chitosan nanoparticles (CS-NPs) significantly enhanced the overall inhibition zone diameter, as well as, the decline in MIC values for Salmonella enterica (50%) and Penicillium chrysogenum (12.5%) was observed. Lactobacillus helveticus CFS, however, displayed lower antimicrobial activity vs. nisin and natamycin, it has both antibacterial and antifungal promising activities.