Not all women 50–74 years received biennial mammography and the situation is worse in rural areas. Accountable care organizations (ACO) emphasize coordinated care, use of electronic health system, and preventive quality measures and these practices may improve their patients’ breast cancer screening rate. Using medical record data of 8,347 women patients aged 50–74 years from eight rural ACO clinics in Nebraska, this study examined patient-, provider-, and county-level barriers and facilitators for breast cancer screening. A generalized estimating equations model was used to account for the correlation among patients from the same provider and county. The multi-level logistic regression results suggest that uninsured non-Hispanic Black patients were less likely to meet the biennial mammography screening guideline. Patients whose preferred language being English, having a preventive visit in the past 12 months, having one or more chronic conditions were more likely to meet the biennial mammography screening guideline. Patients with a primary care provider (PCP) that was male, without a medical doctor degree were less likely to screen biennially. Patients with a PCP that reviewed performance report quarterly, or manually checked patients’ mammography screening status during visits were more likely to screen biennially. Interestingly, patients whose PCP reported being reminded by a care coordination team were less likely to screen biennially. Patients living in counties with more PCPs were also more likely to screen biennially. The study findings suggest that efforts targeting individual and practice-level barriers could be most effective in improving mammography screening for these rural ACO patients.