Neutralization of aerosolized biological threat agents is an important area in the bio-defense research. Novel reactive materials are being developed with the added capability to effectively inactivate viable aerosolized microorganisms. Existing protocols for the evaluation of these new materials do not differentiate between the viability losses caused by heat stress and by combustion products. In this study, a two-configuration experimental approach was developed to address the situations when the bioaerosols is supplied: (i) through the combustion zone so that the microorganisms are exposed to both the thermal and chemical inactivation and (ii) downstream from the combustion zone where the air temperature substantially decreases so that the viability loss occurs primarily due to exposure to combustion products. Two experimental setups were designed and built to implement these configurations. A hydrocarbon fuel flame seeded with three fuel additives, which were delivered to the burner from a powder disperser, represented the tested combustion environments. One of the powders contained aluminum with embedded iodine that was designed to be released at the aluminum melting temperature. In experiments performed with both setups, endospores of Bacillus subtilis var. niger (also referred to as Bacillus atrophaeus or BG spores) were exposed to the combustion environments, and the spore inactivation was quantitatively characterized for each set of conditions using a culturable enumeration of the exposed and non-exposed bioaerosol samples. Additionally, the first configuration was utilized for the tests, in which the burner was replaced with an axial heater providing specific temperature conditions for the challenge bioaerosol with no release of combustion products. It was determined that inactivation levels associated with the heat and chemical stresses may be comparable. It is anticipated that these factors may produce a synergistic effect.