Small ruminant infections with Eimeria spp. cause acute or chronic intestinal problems and significant global economic losses. The present study aimed to determine the prevalence and risk factors of Eimeria spp. infection in goats in Prafi district, Manokwari regency, West Papua province, Indonesia. Fecal samples (n=207) were obtained from 17 farms in Prafi district and evaluated for the existence of oocysts by the Whitlock technique. The overall prevalence of coccidiosis was 90.34% (187/207) and was significantly influenced by the age of the goats with a higher prevalence in young animals under 12 months than in adult animals (>12 months). Five Eimeria spp. were identified such as Eimeria hirci, E. parva, E. christenseni, E. arloingi, and E. alijevi. The univariate analysis result of risk factors indicated that age, rearing system, type of pen, light intensity, and period of cleaning pen were associated with Eimeria spp. infection (P≤0.05). The results of multivariate analysis had three variables associated with infection such as type of pen, light intensity, and rearing system with the highest (OR=45.11) in the type of pen variable. Additionally, to prevent infection, effective management and hygiene procedures must be used based on the risk factors. Understanding these epidemiological infections can help with developing preventative measures, which will lessen the financial impact that these protozoa have on the production of goats.