Microbial infections should be controlled and prevented for successful wound healing and tissue regeneration. Various disinfection methods exist that use antibiotics, ultraviolet (UV), heat, radiation, or chemical disinfectants; however, cold atmospheric pressure plasma has exhibited a unique and effective antibacterial ability that is not affected by antibiotic resistance or pain. This study develops a cold atmospheric pressure microplasma pipette (CAPMP) that outputs an Ar plasma plume through a tube with an inner radius of 180 μm for disinfection in a small area. The CAPMP was evaluated using Staphylococcus aureus and methicillin-resistant Staphylococcus aureus diluted in liquid media, spread on solid agar, or covered by dressing gauze. An increase in the treatment time of CAPMP resulted in a decrease in the number of colonies of the grown microorganism (colony forming unit) and an increase in the disinfected area for both bacteria. The disinfection ability of CAPMP was observed when the bacteria were covered with dressing gauze and was dependent on the number of gauze layers.