Abstract Background Systematic implementation of guidelines for opioid therapy management in chronic non-cancer pain can reduce opioid-related harms. However, implementation of guideline-recommended practices in routine care is subpar. The goal of this quality improvement (QI) project is to assess whether a clinic-tailored QI intervention improves the implementation of a health system-wide, guideline-driven policy on opioid prescribing in primary care. This manuscript describes the protocol for this QI project. Methods A health system with 28 primary care clinics caring for approximately 294,000 primary care patients developed and implemented a guideline-driven policy on long-term opioid therapy in adults with opioid-treated chronic non-cancer pain (estimated N = 3980). The policy provided multiple recommendations, including the universal use of treatment agreements, urine drug testing, depression and opioid misuse risk screening, and standardized documentation of the chronic pain diagnosis and treatment plan. The project team drew upon existing guidelines, feedback from end-users, experts and health system leadership to develop a robust QI intervention, targeting clinic-level implementation of policy-directed practices. The resulting multi-pronged QI intervention included clinic-wide and individual clinician-level educational interventions. The QI intervention will augment the health system’s “routine rollout” method, consisting of a single educational presentation to clinicians in group settings and a separate presentation for staff. A stepped-wedge design will enable 9 primary care clinics to receive the intervention and assessment of within-clinic and between-clinic changes in adherence to the policy items measured by clinic-level electronic health record-based measures and process measures of the experience with the intervention. Discussion Developing methods for a health system-tailored QI intervention required a multi-step process to incorporate end-user feedback and account for the needs of targeted clinic team members. Delivery of such tailored QI interventions has the potential to enhance uptake of opioid therapy management policies in primary care. Results from this study are anticipated to elucidate the relative value of such QI activities.