Destruction of microbial biothreat agents is the subject of increasingly active research in defense and homeland security sectors. Energetic materials are currently being developed with the added capability to effectively inactivate stress-resistant aerosolized microorganisms. In this study, new nano-composites of aluminum and iodine with adjustable powder parameters were developed and tested with respect to their biocidal capabilities. The tests involving inactivation of aerosolized bacterial endospores (Bacillus subtilis) were performed using a state-of-the-art experimental facility, which was designed for assessing the survival of aerosolized microorganisms passed through hydrocarbon fuel flame seeded with various fuel additives. The biocidal capabilities of six different metallic fuel powders (including commercial aluminum and newly-developed nanocomposites) were determined. It was demonstrated that the iodine-containing powder provided a much more effective inactivation of airborne B. subtilis spores than non-iodinated powders. An enhancement factor was in a range of ca. 10 – 100. To distinguish between the effects of thermal and chemical inactivation of airborne endospores exposed to combustion, a series of tests was conducted involving axial heating of the flow of aerosolized endospores in the chamber at different temperature and flow conditions. The association between the inactivation factor and the temperature of exposure for exposure time intervals as short as ca. 0.01 to 0.1 s. Several biological phenomena have been explored to interpret the inactivation data, including denaturation of protein and DNA as well as complex repair mechanisms.