As with all indoor public spaces in Taiwan, the stack rooms in public libraries should meet the air quality guidelines laid down by the Taiwan Environmental Protection Administration. Accordingly, utilizing a university library in Taiwan for experimental purposes, this study investigates the efficiency of gaseous chlorine dioxide (ClO2) as a disinfection agent when applied using three different treatment modes, namely a single-daily disinfection mode (SIM), a twice-daily disinfection mode (TWM), and a triple-daily disinfection mode (TRM). For each treatment mode, the ClO2 is applied using an ultrasonic aerosol device and is performed both under natural lighting conditions and under artificial lighting conditions. The indoor air quality is evaluated before and after each treatment session by measuring the bioaerosol levels of bacteria and fungi. The results show that for all three disinfection modes, the application of ClO2 reduces the indoor bacteria and fungi concentrations to levels lower than those specified by the Taiwan EPA (i.e., bacteria <1500 CFU/m(3), fungi <1000 CFU/m(3)), irrespective of the lighting conditions under which the disinfection process is performed. For each disinfection mode, a better disinfection efficiency is obtained under natural lighting conditions since ClO2 readily decomposes under strong luminance levels. Among the three treatment modes, the disinfection efficiencies of the TWM and TRM modes are very similar under natural lighting conditions and are significantly better than that of the SIM mode. Thus, overall, the results suggest that the TWM treatment protocol represents the most cost-effective and efficient method for meeting the indoor air quality requirements of the Taiwan EPA.