Screening for colorectal cancer (CRC) is widely recommended but underused, even though CRC is the third most diagnosed cancer and the second leading cause of cancer death in the USA. The mPATH™ program is an iPad-based application designed to identify patients due for CRC screening, educate them on the commonly used screening tests, and help them select their best option, with the goal of increasing CRC screening rates. The mPATH™ program consists of questions asked of all adult patients at check-in (mPATH™-CheckIn), as well as a module specific for patients due for CRC screening (mPATH™-CRC). In this study, the mPATH™ program is evaluated through a Type III hybrid implementation-effectiveness design. Specifically, the study consists of three parts: (1) a cluster-randomized controlled trial of primary care clinics comparing a "high touch" evidence-based implementation strategy with a "low touch" implementation strategy; (2) a nested pragmatic study evaluating the effectiveness of mPATH-CRC™ on completion of CRC screening; and (3) a mixed-methods study evaluating factors that facilitate or impede the maintenance of interventions like mPATH-CRC™. The primary objective is to compare the proportion of patients aged 50-74 who are eligible for CRC screening who complete mPATH™-CRC in the 6th month following implementation between the "high touch" and "low touch" implementation strategies. Effectiveness of mPATH™-CRC is evaluated by comparing the proportion who complete CRC screening within 16 weeks of their visit to the clinic between a pre-implementation cohort (8 months before implementation) and a post-implementation cohort (8 months after implementation). This study will provide data on both the implementation of the mPATH™ program and its effectiveness in improving screening rates for CRC. In addition, this work has the potential to have an even broader impact by identifying strategies to support the sustained use of other similar technology-based primary care interventions. ClinicalTrials.gov NCT03843957. Registered on 18 February 2019.