Currently, due to the global pandemic caused by severe acute respiratory syndrome coronavirus SARS-CoV-2, new procedures and devices for effective disinfection of indoor air are of obvious interest. Various studies demonstrated quite broad ranges of the efficiency of essential oils in the control of biological aerosols. This project reports the results of investigation of the antimicrobial activity of essential oils natural for Australia (tea tree oil, eucalyptus oil and lemon myrtle) distributed by newly developed VaxiPod device for various scenarios, including bacterial, viral and fungal inactivation on various surfaces and in aerosol form. It was found that the device was capable of operating continuously over 24-h periods, providing sufficient aerosol concentration to efficiently inactivate microorganisms both on the surface and in airborne form. Twenty-four to forty-eight hours were required to achieve inactivation above 90% of most of the tested microbes on solid surfaces (stainless steel discs and agar plates), whilst similar efficiency of inactivation on fibrous filter surface as well as in aerosol form was achieved over 30–60 min of the process run. The results look very promising for further development of bioaerosol inactivating procedures and technologies for air quality control applications.