Ultraviolet germicidal irradiation (UVGI) technology has garnered substantial attention in disinfecting airborne microorganisms during and beyond the COVID-19 pandemic. Given that UVGI inactivation performance varies in complex in-duct environments, this study examines the effects of bioaerosol particle size and relative humidity (RH) on the inactivation efficiencies of an in-duct UVGI system. MS2 bioaerosols, with phosphate-buffered saline as suspending media and subjected to a bioaerosol drying process, were used in UVGI tests. At any given RH condition (25 %, 40 %, or 60 % RH), lower UV rate constants were presented for larger bioaerosols (2.1–7 μm) in comparison to smaller ones (0.65–2.1 μm). For humidity, the UV rate constant initially increased and then decreased as RH increased from 25 % to 60 %, peaking at 40 % RH, irrespective of the particle size. Notably, the absence of the bioaerosol dryer altered this trend, where the inactivation efficiency decreased with the increase in RH. In conclusion, our findings suggest that a higher UV dose is required to mitigate hazards from larger bioaerosols in very humid environments. In addition, this work proposes a comprehensive flowchart, a beneficial tool for engineers and designers, which facilitates the effective design and implementation of UVGI technology in controlling bioaerosol hazards.