Inactivation of airborne microorganisms due to thermal or chemical air treatment has gained considerable attention. Destruction of aerosolized biothreat agents in environments containing combustion products is particularly relevant to military and counterterrorism situations because some pathogens may survive an explosion or fire in a bio-weapon facility and be dispersed in the atmosphere. Energetic materials with biocidal properties are being sought to effectively inactivate stress-resistant aerosolized microorganisms. Consequently, appropriate methods are needed to test these materials. We designed and built a state-of-the-art experimental facility and developed protocols for assessing the survival of aerosolized microorganisms exposed to combustion. The facility uses a continuous-flow design and includes an aerosolization unit, a test (combustion) chamber, and a measurement system for bioaerosol particles exposed to combustion environments for sub-second time intervals. The experimental method was tested with Bacillus endospores. We assessed the inactivation of aerosolized spores exposed to a gaseous hydrocarbon flame and to combustion of aluminum-based energetic composites (including a novel iodine-containing filled nanocomposite material). Two combustion configurations were evaluated – a vertical strand containing a consolidated material and a specially designed burner in which a fuel powder is fed into a gaseous hydrocarbon flame. It was established that the bioaerosol inactivation may be overestimated due to exposure of spores on collection filters to the combustion products throughout the test. The overestimation can be mitigated by reducing the collection time and minimizing the formation of soot. The experimental facility and method developed in this study enables evaluating effects caused by biocidal products during combustion. The present version of the set-up provides the capability of detecting inactivation levels of ~2.2 × 105 (over five-log viability reduction) its further design modifications can potentially enable measuring bioaerosol inactivation as high as ~107. The method was utilized for establishing feasibility of the new iodine-containing material for microbial agent defeat applications.