Climate change and transboundary air pollution are reshaping atmospheric conditions in Southeast Asia, yet airborne microbiomes remain largely undocumented. The region lacks baseline data, standardised protocols, and integrated frameworks to assess how climate variability and pollution influence microbial composition and function, limiting understanding of microbial transport and climate-sensitive health risks. This project establishes the first Southeast Asian Airborne Microbiome Monitoring Network across Malaysia, Indonesia and Thailand. Using harmonised high-volume air sampling, optimised low-biomass metagenomics and integrate climate–pollution datasets, it will generate the region’s first harmonised baseline dataset on airborne microbial diversity, functional profiles and environmental drivers, providing a scientifically robust regional reference for future multi-site, multi-season, and long-term airborne microbiome monitoring. Machine-learning models will be applied to predict microbiome responses under climate scenarios and develop preliminary microbial exposure indicators. Through regional capacity building, shared protocols, open-access data systems and policy co-design, the project strengthens scientific capability and supports climate-resilient air-quality management and environmental health planning in Southeast Asia.