Purpose This study examines multilevel factors related to colorectal cancer (CRC) screening in a rural Accountable Care Organization (ACO) setting. Methods The study used electronic medical record data from 8 rural ACO clinics in Nebraska. The final sample included 15,866 average‐risk patients aged 50‐75 years who visited participating clinics at least once from June 2014 to May 2015. Logistic regression was conducted to examine simultaneous effects of patient, provider, and county characteristics on CRC screening after accounting for provider‐county‐level correlation using a generalized estimating equations method. Findings The results indicated that patients aged 65 years and older, non‐Hispanic white, whose preferred language was English, who had insurance, who had a wellness visit in the past year, and who had chronic conditions were more likely to be up‐to‐date on CRC screening. Patients were also more likely to be up‐to‐date when their primary care provider was a female medical doctor who was aware of clinic CRC screening protocols or who manually checked patient CRC screening status during the patient visit. Patients in a county with no gastroenterologist, a high poverty rate, and low insurance coverage were less likely to be up‐to‐date on CRC screening. Conclusions  A variety of patient, provider, and county characteristics were associated with CRC screening. Effective strategies to promote CRC screening should address multilevel factors, including: targeting patients with identified individual barriers, modifying physician and clinical practices, and focusing on communities with low socioeconomic status or low levels of medical resources.