This work was to improve antimicrobial activities of horseradish by encapsulated with edible biopolymers such as lecithin and gelatin since it has been difficult to directly use horseradish extracts into foods and food containers due to its strong and undesirable flavors. It was shown that most of the nanoparticles containing the extracts were well formed in round shape with below 400 nm diameter as well as fairly stable and less odd flavors in various pH ranges by measuring zeta potentials. The encapsulation efficiencies of nanoparticles were estimated as 66.6% and 53.4% for lecithin and gelatin, respectively. Minimal Inhibitory Concentration (MIC) of both nanoparticles against G(+), Listeria monocytogenes and G(-), Salmonella typhimurium were also measured as 79 ppm based on AIT concentrations in the extracts, whose activities were about 65% higher than the case of adding crude extract. It was also found that the nanoparticles efficiently penetrated into the cell membrane and started to destruct the cells after 6 hours cultivation under Transmision Electron Microscopy observation. These results prove that the nano-encapsulation of the horseradish extracts can be employed to directly treat into the foods and food containers for antimicrobial purposes with the aids of aerosolization system, by using small amounts of the extracts and having less flavors due to masking effects of nanoparticles.