The behavior of indoor microbial air community is not well understood due to complex functional characteristics of building and environmental stressors. This study aims to understand behavior of microbial air community in relation to work type, height level and environmental factors in a complex built environment. A field survey was conducted at random sites of a research institute. Air microbial (bacteria, fungi & actinomycetes), chemical (PM, NO2, SO2, NH3 & HCOH) and physical (T°C, RH%, noise, lighting & electromagnetic strength) parameters were measured using integrated and real-time instruments. The overall microbial concentrations averaged 4451 CFU/m3 (95% CI: 3795-5107 CFU/m3), 916 CFU /m3 (95% CI: 745-1087 CFU /m3), 556 CFU /m3 (95% CI: 473-639 CFU/m3) and 197 CFU/m3 (95% CI: 140- 254 CFU/m3) for environmental bacteria, mesophilic bacteria, fungi and actinomycetes, respectively. Global index of microbial contamination was significantly high at the hospital and near surface ground level. Amplification index of microbial concentration was ≥1.5 at 14% of total sites. Microbial concentrations decreased with increasing height level. Environmental stressors had complex interactions with microbial concentrations. Multiple linear regressions showed that ventilation influenced environmental bacteria. RH% and PM positively influenced mesophilic bacteria and fungal concentrations, respectively. Standardizing environmental factors could control microbial community in buildings.