Bioaerosols, such as bacterial and fungal cells and their spores, are components of indoor airborne particulate matter and have been associated with human health problems as well as various environmental issues. Natural antimicrobial products have been used in air filters for bioaerosol control. However, natural products may lose some function due to their sensitivity to environmental factors such as temperature and humidity. In this study, we investigated the effects of temperature on antimicrobial fiber filters coated with nanoparticles of a natural product, namely, Sophora flavescens extract. Inactivation efficiency decreased with increasing temperature and treatment time. A quantitative chemical analysis of the filters revealed that the quantities of antimicrobial compounds decreased noticeably, with a consequent decrease in antimicrobial activity. In addition, the S. flavescens nanoparticles on the filter fiber surface melted gradually as treatment time increased at temperatures >100• C. This change in nanoparticle morphology in turn affected the pressure and filtration efficiency of filters, both of which decreased with increasing temperature and treatment time. These results could provide a scientific basis for the improvement of indoor air-quality control using antimicrobial air filters coated with S. flavescens nanoparticles.