In Ethiopia, several studies have reported the occurrence of Cryptosporidium infection in young calves, lambs, and HIV positive patients. However, studies on cattle and sheep of all age categories, and humans (farm workers and animal owners) were limited. A cross-sectional study design was thus conducted from October 2021 to April 2022 to study the occurrence of Cryptosporidium in dairy cattle, sheep, humans, and manure in and around Adama and Asella towns, Oromia, Ethiopia. Dairy cattle and sheep were stratified according to their age and randomly sampled. Stool samples from volunteered farm workers and household members were collected purposefully. A semi-structured questionnaire was also used to collect information about manure handling practices. All samples (dairy cattle = 234, sheep = 200, humans = 56, manure = 58) were processed with sugar floatation technique and the modified Ziehl-Neelsen staining method. A univariate regression analysis was used to test the association of individual factors with the occurrence of Cryptosporidium. Associated factors were subjected to multivariate regression analysis to identify potential risk factors. The overall prevalence of Cryptosporidium in dairy cattle, sheep, humans, and manure was 20.5%, 14%, 16%, and 13.20%, respectively. The occurrence of Cryptosporidium infection in dairy cattle at the ages of 1–12 months and 13–36 months was 3.48 and 3.07 times higher, respectively, in comparison to the age above 36 months. Similarly, the occurrence was 2.69 times higher in sheep aged 1–6 months than in those aged older than 6 months. And also, a higher average level of oocyst count (above 10 oocysts) per-field was examined in dairy cattle (3/48) aged 1–12 months, followed by sheep (1/28) aged 1–6 months. Furthermore, the likelihood of infection was 13 times greater in farm workers compared with the rural farmer members. In addition, the occurrence of oocysts was 22.8 times higher in manures from dairy cattle than manure from sheep. From data on manure handling practices, only 16.8% of them had manure storage holes, 98.1% used manure for crop production, and all of them used manure without treatment. The current study revealed the occurrence of Cryptosporidium infection in all age groups of dairy cattle and sheep, farm workers, animal owners, and manures. Therefore, more studies on adult animals and manure is required to investigate their contribution to environmental contamination as well as their role as a source of infection in young calves and lambs. In addition, molecular characterization is also required to identify the zoonotic species of Cryptosporidium.