Aeroecology, a field emerging since its conceptualization in 2008 and rooted in World War II radar technology, explores the ecological dynamics of the aerosphere. This interdisciplinary field holds promise for understanding pollution, disease transmission, and agricultural pest management. While the aerosphere comprises biotic and abiotic components influencing aerosol microbiome composition, gaps remain in characterizing bioaerosols, particularly amidst climate change challenges. This study investigates the impact of urbanization, specifically heat and cool island effects, on airborne microorganisms. We hypothesized that aerosol microbial richness, diversity, and evenness would vary with the time and location of heat and cool island effects. In La Verne, we observed changes in microbial richness related to heat and cool island effects with respect to time of day (p = 0.0001) and the interaction between time of day and location (p = 0.0331). However, microbial diversity and evenness remained unaffected by time of day, location, or the interaction between these factors (p > 0.05 respectively). Notably, the south campus of the University of La Verne exhibited the highest aerosol microbial richness (p ≪ 0.001), whereas Las Flores Park displayed significant changes in aerosol microbial richness between the (morning) urban cool island effect and (afternoon) urban heat island effect (p = 0.02). Our findings emphasize the need for further research on aerosol microbiome dynamics in urban environments to better understand their impacts on human health and the environment, contributing to sustainable urban planning.