Coccidiosis is an enteric disease caused by protozoa of the Eimeria genus and is of great economic relevance in industrial aviculture. The objective of this work was to determine the prevalence of Eimeria sp. in broiler poultry houses with positive (System 1) and negative (System 2) pressure ventilation and assess the associated factors. A transversal study was conducted using 8 random broiler chickens from 64 houses (n = 512) and macroscopic and histologic evaluation of the intestines, as well as PCR for Eimeria sp. The prevalence of Eimeria sp. was 90.6% (95% confidence interval [CI]: 97.8–83.5), with 93.8% (95% CI: 100–85.4) in System 1 and 87.5% (95% CI: 99.0–76.0) in System 2. The most prevalent species was Eimeria acervulina, and the most common combination was Eimeria acervulina, Eimeria maxima, and Eimeria tenella. System 2 and the negative Eimeria subgroup showed the best results for feed conversion and daily weight gain. By evaluating litter treatment, we found that quicklime reduced the risk of presence of Eimeria maxima and Eimeria tenella. In conclusion, Eimeria sp. had a high prevalence in both systems, with a predominance of mixed infections. System 2 and negative flocks showed the best zootechnical results.