Background Oil spills are ranked among the greatest global challenges to humanity. In Uganda, owing to the forthcoming full-scale production of multi-billion barrels of oil, the country’s oil pollution burden is anticipated to escalate, necessitating remediation. Due to the unsuitability of several oil clean-up technologies, the search for cost-effective and environmentally friendly remediation technologies is paramount. We thus carried out this study to examine the occurrence of metabolically active indigenous bacterial species and chemical characteristics of soils with a long history of oil pollution in Uganda that can be used in the development of a bacterial-based product for remediation of oil-polluted sites. Results Total hydrocarbon analysis of the soil samples revealed that the three most abundant hydrocarbons were pyrene, anthracene and phenanthrene that were significantly higher in oil-polluted sites than in the control sites. Using the BIOLOG EcoPlate™, the study revealed that bacterial species richness, bacterial diversity and bacterial activity (ANOVA, p p Conclusions This study revealed largely similar bacterial community profiles between the oil-polluted and control sites suggestive of the occurrence of metabolically active bacterial populations in both sites. The oil-polluted sites had higher petroleum hydrocarbon, heavy metal, nitrogen and phosphorus contents. Even though we observed similar bacterial community profiles between the oil polluted and control sites, the actual bacterial community composition may be different, owing to a higher exposure to petroleum hydrocarbons. However, the existence of oil degrading bacteria in unpolluted soils should not be overlooked. Thus, there is a need to ascertain the actual indigenous bacterial populations with potential to degrade hydrocarbons from both oil-polluted and unpolluted sites in Uganda to inform the design and development of a bacterial-based oil remediation product that could be used to manage the imminent pollution from oil exploration and increased utilization of petroleum products in Uganda.