Metritis has considerable economic impact on dairy herd profitability due largely to reduced reproductive performance. Studies in Ethiopia only report prevalence, with no available data on the incidence of metritis. The present prospective cohort study aimed to estimate the incidence of puerperal metritis, identify risk factors, and isolate the causative bacteria in dairy cows in Hawassa. Daily follow-up of 120 dairy cows from parturition to 21 days postpartum was carried out from November 2019 to February 2021. Of these, 21 developed puerperal metritis with an incidence rate of 0.94 cases per 100 cow days at risk (95 % CI: 0.6–1.4). The cumulative incidence was found to be 17.5 % (95 % CI: 11.8–25.6). Over 90 % of the puerperal metritis occurred within the first 10 days of parturition. The mean day of occurrence of puerperal metritis was 7.7 days postpartum and the mean rectal temperature in metritic cows was 40.5 °C. Retained fetal membranes (RFM) (p < 0.001) emerged as the only predisposing factor for metritis in the final Cox regression model. Cows with RFM faced a 14.9 times higher risk of metritis compared to cows without RFM. A total of 52 bacterial isolates, belonging to 4 genera, were recovered from the aerobic culture of 21 uterine swab samples. E. coli and Staphylococcus spp. were the most frequently isolated bacteria, with recovery from 21 (100 %) and 20 (95.2 %) of the metritic uteri, respectively. Results of this study suggested the importance of reducing incidence of RFM to reduce incidence of metritis in dairy cows.