Introduction Eimeria infection is one of the protozoal diseases of animals caused by various species of Eimeria (intracellular parasite) and causes reduced productivity and mortality in ruminants, especially in young ones. Despite the fact that the disease is one of the leading causes of economic losses, there is little information in Ethiopia on the occurrence of the infection in cattle and sheep. Methods A cross-sectional study was conducted from December 2021 to April 2022 in and around Adama and Bishoftu towns with the objectives to estimate the prevalence of Eimeria infection; identify circulating Eimeria oocysts, the intensity/burden of infection and associated risk factors of Eimeria infection in cattle and sheep. A total of 384 randomly selected (265 cattle and 119 sheep) fecal samples were collected from the rectum and examined by flotation technique using sheather’s sugar solution to detect the oocysts of Eimeria . A 2.5% potassium dichromate solution was added to the positive fecal samples for sporulation of the oocysts. Results and discussion The overall prevalence of 48.95% Eimeria infection was recorded during the study. 45.0% and 58% prevalence of the infection was registered in cattle and sheep, respectively. There was a statistically significant difference (P ˂ 0.05) in Eimeria infection between the study animal species, age of the animals, breed, farm hygiene and management system. However, there was no significant difference in Eimeria infection (P > 0.05) in sex, body condition of the animals and fecal consistency. The maximum oocysts per gram of feces was found to be 10,000. Eimeria infection is of great importance to livestock producers and requires serious control and prevention initiatives.