BACKGROUND: In this paper we describe the use of the Consolidated Framework for Implementation Research (CFIR) to study implementation of a web-based, point-of-care, EHR-linked clinical decision support (CDS) tool designed to identify and provide care recommendations for adults with prediabetes (Pre-D CDS). METHODS: As part of a large NIH-funded clinic-randomized trial, we identified a convenience sample of interview participants from 22 primary care clinics in Minnesota, North Dakota, and Wisconsin that were randomly allocated to receive or not receive a web-based EHR-integrated prediabetes CDS intervention. Participants included 11 clinicians, 6 rooming staff, and 7 nurse or clinic managers recruited by study staff to participate in telephone interviews conducted by an expert in qualitative methods. Interviews were recorded and transcribed, and data analysis was conducted using a constructivist version of grounded theory. RESULTS: Implementing a prediabetes CDS tool into primary care clinics was useful and well received. The intervention was integrated with clinic workflows, supported primary care clinicians in clearly communicating prediabetes risk and management options with patients, and in identifying actionable care opportunities. The main barriers to CDS use were time and competing priorities. Finally, while the implementation process worked well, opportunities remain in engaging the care team more broadly in CDS use. CONCLUSIONS: The use of CDS tools for engaging patients and providers in care improvement opportunities for prediabetes is a promising and potentially effective strategy in primary care settings. A workflow that incorporates the whole care team in the use of such tools may optimize the implementation of CDS tools like these in primary care settings. Trial registration Name of the registry: Clinicaltrial.gov. TRIAL REGISTRATION NUMBER: NCT02759055. Date of registration: 05/03/2016. URL of trial registry record: https://clinicaltrials.gov/ct2/show/NCT02759055 Prospectively registered.