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Background Despite the high prevalence of comorbid chronic pain and depression, this comorbidity remains understudied. Meditation has demonstrated efficacy for both chronic pain and depression independently, yet there have been few studies examining its effectiveness when both conditions are present concurrently. Furthermore, while meditation is generally accepted as a safe and effective health intervention, little is known about how to implement meditation programs within or alongside the health care system. Methods We will conduct a hybrid type 1 effectiveness–implementation evaluation. To measure effectiveness, we will conduct a randomized controlled trial comparing Sahaj Samadhi Meditation and the Health Enhancement Program in 160 people living with chronic pain, clinically significant depressive symptoms, and on long-term opioid therapy. Changes in depressive symptoms will be our primary outcome; pain severity, pain-related function, opioid use, and quality of life will be the secondary outcomes. The primary end point will be at 12 weeks with a secondary end point at 24 weeks to measure the sustainability of acute effects. Patients will be recruited from a community-based chronic pain clinic in a large urban center in Mississauga, Canada. The meditation program will be delivered in the clinical environment where patients normally receive their chronic pain care by certified meditation teachers who are not regulated health care providers. We will use a mixed-methods design using the multi-level framework to understand the implementation of this particular co-location model. Discussion Results of this hybrid evaluation will add important knowledge about the effectiveness of meditation for managing depressive symptoms in people with chronic pain. The implementation evaluation will inform both effectiveness outcomes and future program development, scalability, and sustainability. Trial registration ClinicalTrials.gov: NCT04039568. Registered on 31 July 2019.