This study examined the influence of carrot disinfection with electrolyzed acidic water (EAW) on the distribution of microorganisms on each tissue, the changes in microorganisms distribution during storage, and effective disinfection methods using carrot sections. When carrots were disinfected by dipping in EAW, total viable bacterial counts (TVBC) in the cortical layer as well as in the phloem and xylem decreased. During storage, the TVBC in each part of the carrot increased; however the increase was delayed in disinfected carrots. The highest disinfection effect on carrot sections prepared from the cortical layer, phloem, and xylem was observed with sodium hypochlorite solution, followed by EAW, and then purified water. Substitution of air in the intercellular spaces of the phloem and xylem with EAW enhanced this disinfection effect, resulting in a significant reduction of in TVBC in the xylem section. This substitution also increased CO2 production.