Introduction: In-theater inhalation exposure to burn pit emissions (BPEs) and sand has been linked to respiratory issues, prompting a study to identify molecular alterations and potential biomarkers related to exposure and outcomes. Methods: Using a complex Results: Both BPE and BPE + Sand exposures significantly altered the lung microbiome, demonstrating increased mean alpha diversity and the highest number of unique ASVs. These changes in the lung microbiome began as early as 4 days post-exposure and continued throughout 90 days post-exposure. BPE and BPE + Sand groups had increased levels of Discussion: These data indicate that BPE exposure significantly alter the lung microbiome, whereas sand inhalation exposures alone did not seem to cause significant changes, nor did they provide an additive effect when combined with BPE. While the sub-chronic exposure study design led to more subtle molecular alterations in the lung tissue than expected, BPE exposures resulted in distinct and significant microbiome compositional changes in the lung. The observed population shift provided a signature specific to the type of inhalation exposure. Further efforts could lead to an understanding of the role of individual lung microbiomes in inhalation exposure risks and outcomes.