Air pollution is a fourth most hazardous global risk factor for human health. In 2019 alone, 192 million years of human life lost were due to air pollution exposures. Among other health adverse effects, inhaling polluted air compromises gene expression and commensal microbiota. We investigate the effects of a polluted air by challenging fruit flies with a common chemical found in polluted air around the world, Benzo[a]pyrene. We study intergenerational effects of air pollution on brain- and head-specific gene activity and the host microbiome composition. As females and males respond to air pollution stress differently, our goal is to quantify the stress response in each sex. This work provides a deeper understanding of the multifaceted air pollution effects on public health.