Background In Ethiopia, there is not enough information about indoor air bacterial pollution. Therefore, this study aimed to determine bacterial indoor air pollution and its associated risk factors among residences of Gondar town. Methods A cross-sectional survey of indoor air pollution was conducted on 259 selected houses from February to May 2019. Sociodemographic and housing characteristics were collected using a questionnaire and checklist. Passive settle plate method using blood culture media was employed to collect samples and identification of isolates done by both quantitative and qualitative analysis. Results A total of 259 houses were investigated, and 13 different types of bacterial species were isolated. Of these, Bacillus species 259 (100%) and coagulase-negative Staphylococcus species 101 (34.4%), Enterobacter cloacae, Klebsiella species, Citrobacter diversus, Escherichia coli, and Pantoea species were isolates. Tetracycline and cotrimoxazole were ineffective, but ciprofloxacin and ceftriaxone were efficient antibiotics. Educational status, presence of domestic animals within the house, and integrated toilets were significantly associated with indoor bacterial pollution ( p < 0.05). Conclusion Indoor air pollution was higher in this study than international quantification limit (5 colony-forming unit/4 h) of clean rooms. So, periodic surveillance of indoor air quality and assessing risk factors should be addressed to assess the burden and intervene accordingly.