The term “built environment” refers to the natural surroundings that humans have created, including buildings, transportation networks, and other manmade areas where people spend the majority of their time. These environments host distinct microbial populations that are substantially distinct from those that prevail in other natural settings. Despite the diversity of microorganisms in the built environment, there is limited understanding of the makeup of these complex microbial communities and their impact on human health. To date, there has been no comprehensive bibliometric overview of the microbiomes of the built environment. Therefore, the aim of this research paper is to conduct a comprehensive bibliometric analysis of the microbiomes of the built environment by identifying research trends and future directions shaped by the COVID-19 pandemic, while highlighting emerging themes and providing guidance for future interdisciplinary research that integrates microbial science with public health, urban design, and sustainability. A specialized search query has been formulated to extract the relevant literature from the Scopus database, resulting in the identification of 520 papers published between 1992 and 2024. The topic has gained momentum in the past two decades with a notable increase following the COVID-19 pandemic. These results emphasize the growing interest and research being dedicated to comprehending the microbiomes of the built environment. The rise in publications, especially from the USA, demonstrates how crucial this field is to addressing issues related to public health in the design of the built environment. Future research should focus on elucidating the ecological functions of these microbial communities and their repercussions on public health, which could regulate the design and management of healthy built environments.