The use of microwaveplasma for sterilization is relatively new. The advantages of this method are the relatively low temperature, time-savings and its nontoxic nature, in contrast to traditional methods such as heat and gas treatment, and radiation. This study investigated the sterilization effects of microwave-induced argon plasma at atmospheric pressure on materials contaminated with various microorganisms, such as bacteria and fungi. A low-cost and reliable 2.45 GHz, waveguide-based applicator was designed to generate microwaveplasma at atmospheric pressure. This system consisted of a 1 kW magnetron power supply, a WR-284 copper waveguide, an applicator including a tuning section, and a nozzle section. Six bacterial and fungal strains were used for the sterilization test. The results showed that regardless of the strain, all the bacteria used in this study were fully sterilized within 20 seconds and all the fungi were sterilized within 1 second. These results show that this sterilization method is easy to use, requires significantly less time than the other traditional methods and established plasma sterilization methods, and it is nontoxic. It can be used in the field of sterilization in medical and dental clinics as well as in laboratory settings.