Airborne microorganisms, which are currently termed bioaerosols, have received attention owing to the harmful effects they have on human health. As the concern over airborne microorganisms grows, there also grows an urgent need to study and develop efficient methods for controlling them. In this study, thermal energy using a thermal tube was tested as a control method, mainly against airborne E. coli. For a comparison, B. subtilis var. niger spores were utilized in the experimentation. It was found that the widely known inactivation conditions for microorganisms were not adequate against airborne microorganisms. The experimental results demonstrated the need for extensive studies that should investigate adequate and economic conditions to control against airborne bacteria. In this study, thermal energy exposed by the thermal tube demonstrated an inactivation performance for controlling E. coli bioaerosols.