The varroa mite (Varroa destructor) is the most economically important parasitic pest of honey bees (Apis mellifera) that causes global colony decline and loss. Since its first detection in Ethiopia in 2010, little is known about the current infestation levels and contributing factors to the mite's distribution across the country. In this study, we conducted a large‐scale assessment of varroa prevalence and infestation levels in managed colonies across three potential beekeeping regions of Ethiopia; Oromia, Amhara and Southern Nations, Nationalities and Peoples Region (SNNPR). A total of 360 samples from 39 apiaries were collected following standard protocols and the mite prevalence and infestation levels were determined using the established method of varroa research. Overall, 89% of sampled colonies were infested by the mite, with varying prevalence rates across the regions: 95.8% in Oromia, 85.2% in Amhara and 71.9% in SNNPR, indicating the widespread nature of the parasite throughout the country. The varroa infestation levels were lower in local hives (2.6 ± 5.9) than in frame hives (5.0 ± 0.9), and significantly higher in brood bees (5.6 ± 0.8) than in adult bees (1.93 ± 0.17) (p < 0.001). Possible factors contributing to the varied mite prevalence and infestation levels in the country include differences in agro‐ecology, beekeeping practices, host age preference and the nature of bee hives. Therefore, our study provides insights into the current status of varroa prevalence and associated factors across regions in Ethiopia. Further investigation is required to explore the probable impact of the parasite on the health and productivity of local honey bees, in order to design future monitoring strategies.