The land-use configuration has huge impact on emission sources and also a major influencing factor, which ultimately determine the microbial count, composition and seasonal dynamics of bioaerosols at respective site. Despite this, very few studies compare bioaerosols exposure at different land-use sites. The aim of the present study was to measure and compare the aerosolised bacterial and fungal counts across seasons using active Anderson cascade impactor at different land-use configurations in an urban metropolitan. The counts of aerosolised bacteria and fungi were estimated across five seasons of a tropical climate. A mixed-effect model showed that the season and land-use configuration have a bearing on microbial counts. Season and land use interact in a complex manner to produce bioaerosol count variability. Meteorological parameter (temperature and relative humidity) had a significant effect on microbial counts at all land-use configurations, but they could not fully explain variations of microbial counts in the mixed model.