Pathogenic Escherichia coli, Salmonella spp. and Campylobacter spp. are bacteria associated with foodborne diseases. This systematic review and meta-analysis investigates the prevalence of these pathogens in foods sold across seven East African Community (EAC) countries and identifies key risk factors for contamination. A comprehensive search for peer-reviewed papers and grey literature was conducted in six databases (PubMed, CAB Direct, African Journals Online, Google Scholar, ScienceDirect, and Web of Science), as well as 12 online repositories. The review encompassed studies published in English and French between January 2000 and June 2022, adhering to the 2020 guidelines for the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Eligible studies employed probabilistic sampling and reported the proportion of contaminated samples. Out of 4134 initial records, 53 studies met the inclusion criteria. Most were conducted in Kenya (n = 22) and Tanzania (n = 21), with no eligible studies found for Burundi and South Sudan. E. coli and Salmonella spp. were the most frequently studied pathogens, while Campylobacter spp. was less represented. Using a random-effects model in Stata®, pooled prevalence estimates were 41 % for E. coli (95 % CI: 34–52 %), 12 % for Salmonella spp. (95 % CI: 12–27 %), and 9 % for Campylobacter spp. (95 % CI: 7–32 %). Significant heterogeneity was observed and further explored through meta-regression and subgroup analyses. Contamination levels varied by food type, processing status, sample size, and country. Meat, especially poultry, showed the highest prevalence of bacterial contamination across all pathogens. Alarmingly, beverages were also highly contaminated, with E. coli detected in 66.3 % (95 % CI: 31–89 %) and Salmonella spp. in 11.8 % (95 % CI: 1–55 %) of samples. Key risk factors included poor hygiene practices, inadequate sanitation, high storage temperatures, and a lack of food safety training. These findings underscore the urgent need for improved food safety measures in the EAC region for improved public health and support trade advancement. The study also highlights critical gaps in surveillance, particularly for Campylobacter spp., pathogenic E. coli, and data from some EAC countries.