Monitoring indoor and outdoor bioaerosol concentrations is essential for environmental management and evaluation of the health impact of air pollution. This study assessed indoor and outdoor microbial air quality for two cities of the Sistan region in Iran, Zabol and Zahak, in summer (July and August) and autumn (October and November) of 2022. Indoor air quality was compared between two rooms with varying conditions associated with windows (living room: windows opened to the north and to the prevailing wind; bedroom: opened to the south and opposite to the prevailing wind). Bacterial concentrations were monitored using the settle plate method inside and outside household environments at 6:30 a.m., 10:30 a.m., 4:30 p.m., 7:30 p.m., and 12:30 a.m. Zahak exhibited higher PM10 and bacterial concentrations compared to Zabol. Bacterial concentrations in the outdoor environment were significantly higher than those in indoor air and also higher in summer than autumn in both cities. There was no significant difference in indoor air samples between the two rooms (p> 0.05) in Zabol, indicating that the bacteria pollution was similar in the two rooms. Diurnal and day-to-day patterns of airborne bacteria were similar in indoor and outdoor air, consistent with PM10 variations, pointing to the association between outdoor and indoor air quality. PM10 and bacterial concentrations peaked at 10:30 a.m. and were lowest at 4:30 p.m. Results of this study have implications for other dust-prone cities of the world and offer a valuable dataset for bacterial concentrations to compare with other regions of the world.