Background: Within health promotion research, there is a need to assess strategies for integration and scale up in primary care settings. Hybrid interventions that combine clinical effectiveness trials with implementation studies can elicit important contextual information on facilitators and barriers to integration within a health care system. This article describes lessons learned in developing and implementing a qualitative study of a cluster-randomized controlled trial (RCT) to reduce cardiovascular disease (CVD) among people with diabetes in Sonora, Mexico, 2015-2019. Methods:The research team worked cooperatively with health center personnel from 12 Centers that implemented the intervention. The study used observations, stakeholder meetings, case studies, staff interviews and decision maker interviews to explore issues such as staff capacity, authority, workflow, space, and conflicting priorities, as well as patients' response to the program within the clinical context and their immediate social environments. Applying a multi-layered contextual framework, two members of the research team coded an initial sample of the data to establish inclusion criteria for each contextual factor. The full team finalized definitions and identified sub nodes for the final codebook. Results: Characteristics of management, staffing, and the local environment were identified as essential to integration and eventual adoption and scale up across the health system. Issues included absence of standardized training and capacity building in chronic disease and health promotion, inadequate medical supplies, a need for program monitoring and feedback, and lack of interdisciplinary support for center staff. Lack of institutional support stemming from a curative vs. preventive approach to care was a barrier for health promotion efforts. Evolving analysis, interpretation, and discussion resulted in modifications of flexible aspects of the intervention to realities of the health center environment. Conclusion: This study illustrates that a robust and comprehensive qualitative study of contextual factors across a social ecological spectrum is critical to elucidating factors that will promote future adoption and scale up of health promotion programs in primary care. Application of conceptual frameworks and health behavior theory facilitates identification of facilitators and barriers across contexts. Trial registration: www.ClinicalTrials.gov, identifier: NCT02804698 Registered on June 17, 2016.

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