Colorectal cancer (CRC) screening has been shown to decrease CRC mortality, yet significant disparities persist among those living in rural areas, from minority backgrounds, and those having low income. The purpose of this two-arm randomized controlled trial is to test the effectiveness and fidelity of a stepped care (increasing intensity as needed) approach to promoting 3-year adherence to CRC screening via fecal immunochemical testing (FIT) or colonoscopy in rural community clinics serving high rates of low-income and minority patients. We hypothesize that, compared to enhanced usual care (EUC), patients receiving the multifaceted CRC screening intervention will demonstrate higher rates of CRC screening completion over 3 years. Participants from six federally qualified health centers (FQHCs; N = 1200 patients) serving predominately low-income populations in rural Louisiana will be randomized to the intervention or EUC arm. All participants will receive health literacy-directed CRC counseling, simplified materials about both the FIT and colonoscopy procedures, and motivational interviewing to aid in the determination of test preference. Participants in the intervention arm will also receive motivational reminder messages from their primary care provider (via audio recording or tailored text) for either a scheduled colonoscopy or return of a completed FIT. Participants in the EUC arm will receive the standard follow-up provided by their clinic or colonoscopy facility. The primary outcome will be completion of either colonoscopy or annual FIT over 3 years. Results will provide evidence on the effectiveness of the intervention to decrease disparities in CRC screening completion related to health literacy, race, and gender.Trial registration:Clinicaltrials.gov Identifier NCT04313114