Background: Indoor air pollution, including airborne microorganisms, can cause allergies, respiratory diseases, and immune-toxic diseases. Sneezing generates millions of airborne microbial infections, and ventilation sources alter microbial communities. Few studies exist in developing countries, including Ethiopia, and Harar Town. The aim is to assess microbial indoor air quality and associated factors among private clinics, Harar town, Eastern Ethiopia. Methodology: A cross-sectional study was conducted on 260 private clinic rooms in Harar town, using a systematic random sampling method and passive air sampling. Data was collected using the settle plate method and an observation checklist. Bivariate and multivariate analysis was performed using binary logistic regression, with a P-value of <0.05 considered statistically significant. Result: The minimum and maximum bacterial loads were 3933 CFU/m3 and 92 CFU/m3 respectively. Based on the pollution degree of the European Commission, the Mean bacterial load (904 CFU/m3) was at higher bacterial load. The highest, lowest, and mean fungal loads were 1967 CFU/m3, 9 CFU/m3 and 401 CFU/m3 respectively. Temperature of <25 °C (AOR = 1.58, p = 0.04, and 95% CI = 1.05, 1.91), >28 °C (AOR = 1.23, P = 0.03, and 95% CI = 1.51, 2.02) were significantly associated with bacterial indoor air quality. Relative humidity of treatment rooms (AOR = 1.87, p = 0.02, and 95% CI = 1.21, 3.09) had an association with bacterial loads. The clinic treatment rooms with a recorded temperature <25 °C (AOR = 6.32, p = 0.01, and 95% CI = 6.10, 8.25) had associated with fungal loads. But the rooms having a temperature of >28 °C (AOR = 0.41, p = 0.04, and 95% CI = 0.31, 0.78) were 59% less likely to comply with the fungal standards compared to rooms having a temperature of 25–28 °C. The clinic rooms with a relative humidity of <30% (AOR = 7.75, p = 0.02, 95% CI = 7.21, 8.39) were 7.75 times more likely to comply with those with a relative humidity of > 60% in the treatment rooms. Conclusion: Private clinics in Harar had a moderate fungal load and a higher indoor air bacterial concentration when compared to different indoor air standards. Temperature, humidity, inadequate ventilation and the presence of unsanitary attached toilets are some variables associated with microbial loads.