Slaughterhouses are certified premises where animals are slaughtered and inspected to ensure meats are wholesome and safe for public consumption. To determine the common zoonoses encountered in a municipal slaughterhouse of Abeokuta, Ogun State, Nigeria, a three-year retrospective study was conducted (2014–2016). During the review of slaughterhouse records, the overall throughput of cattle slaughtered was 146,794 (4077.6 ± 413.6; 95% confidence interval [CI] 3923.3–4206.7). Female animal slaughtering outweighed male ones at 5:1 ratio (p < 0.0001). The highest number of cattle were slaughtered in December 2014, December 2015, and August 2016. Of all the total cattle slaughtered, the overall observed prevalences for bovine tuberculosis (BTB), hydatidosis and fasciolosis were estimated as 9514 (6.5%, 264.3 ± 81.7; 95% CI 236.6–291.9), 1851 (1.3%, 55.8 ± 17.3; 95% CI 49.9–61.6) and 845 (0.6%, median = 19.0; 95% CI 18.7–28.3), respectively. On average the highest number of BTB cases was reported in February-March, it declined slightly in October and increased again in November. Similarly, the highest numbers of hydatidosis and fasciolosis were observed in March and February, respectively. A significant (p = 0.02) mean variation of cases of BTB was found across the period and it was higher (p = 0.03) during the wet/rainy season in 2015. Our results emphasized the need to promote coordinated active surveillance for zoonoses detection and mitigation to ensure food safety at farm and slaughterhouse levels. Adequate record keeping for specific organ/meat/carcass condemnation is crucial at postmortem, as this represents a significant loss of animal proteins and revenues. Such data can be used for informed policy to intensify reduction in economic loss associated with animal diseases.