Many studies have shown that pet shops have a high concentration of bioaerosols. Thus, effective disinfection protocols are essential to protect the pet shop staff and visitors to the store. The present study examines the effectiveness of gaseous chlorine dioxide (ClO2) fogging in minimizing the residual bacteria and fungi levels in a typical pet shop in Taiwan consisting of a commodity area, a lodging area, and a grooming area. This investigation uses three disinfection modes (DMs) according to different disinfection periods, namely once every hour (1DM), once every 2 h (2DM), and once every 3 h (3DM). The bacteria and fungi concentrations are measured before and after disinfection treatment, and the effectiveness of each disinfection mode is evaluated using standard statistical techniques. To assess the effect of the environmental factors on the disinfection efficiency, measurements are taken of temperature, relative humidity, airflow velocity, the carbon dioxide concentration, the PM1, PM2.5, PM7, PM10, and TSP level at each sampling locations. The results reveal that the effectiveness of the three disinfection modes depends on both the environmental parameters and the use of the three areas (e.g., commodity, lodging, or grooming). Hence, the choice of disinfection method should be adjusted accordingly. For all three disinfection modes, a faster air velocity is beneficial in spreading the disinfectant throughout the indoor space and improving the disinfection performance. Overall, the results presented in this study confirm that gaseous chlorine dioxide disinfection improves the air quality in the pet shop interior, and thus beneficial in safeguarding the health of the pet shop staff and visitors.