Background Digital diabetes prevention programs (dDPPs) are effective behavior change tools to prevent disease progression in patients at risk for diabetes. At present, these programs are poorly integrated into existing health information technology infrastructure and clinical workflows, resulting in barriers to provider-level knowledge of, interaction with, and support of patients who use dDPPs. Tools that can facilitate patient-provider interaction around dDPPs may contribute to improved patient engagement and adherence to these programs and improved health outcomes. Objective This study aims to use a rigorous, user-centered design (UCD) methodology to develop a theory-driven system that supports patient engagement with dDPPs and their primary care providers with their care. Methods This study will be conducted in 3 phases. In phase 1, we will use systematic UCD, Agile software development, and qualitative research methods to identify key user (patients, providers, clinical staff, digital health technologists, and content experts) requirements, constraints, and prioritization of high-impact features to design, develop, and refine a viable intervention prototype for the engagement system. In phase 2, we will conduct a single-arm feasibility pilot of the engagement system among patients with prediabetes and their primary care providers. In phase 3, we will conduct a 2-arm randomized controlled trial using the engagement system. Primary outcomes will be weight, BMI, and A1c at 6 and 12 months. Secondary outcomes will be patient engagement (use and activity) in the dDPP. The mediator variables (self-efficacy, digital health literacy, and patient-provider relationship) will be measured. Results The project was initiated in 2018 and funded in September 2019. Enrollment and data collection for phase 1 began in September 2019 under an Institutional Review Board quality improvement waiver granted in July 2019. As of December 2020, 27 patients have been enrolled and first results are expected to be submitted for publication in early 2021. The study received Institutional Review Board approval for phases 2 and 3 in December 2020, and phase 2 enrollment is expected to begin in early 2021. Conclusions Our findings will provide guidance for the design and development of technology to integrate dDPP platforms into existing clinical workflows. This will facilitate patient engagement in digital behavior change interventions and provider engagement in patients’ use of dDPPs. Integrated clinical tools that can facilitate patient-provider interaction around dDPPs may contribute to improved patient adherence to these programs and improved health outcomes by addressing barriers faced by both patients and providers. Further evaluation with pilot testing and a clinical trial will assess the effectiveness and implementation of these tools. Trial Registration ClinicalTrials.gov NCT04049500; https://clinicaltrials.gov/ct2/show/NCT04049500 International Registered Report Identifier (IRRID) DERR1-10.2196/26750