Lean is a leading change strategy used in health care to achieve short-term efficiency and quality improvement while promising longer-term system transformation. Most research examines Lean intervention to address isolated problems, rather than to achieve broader systemic changes to care delivery. Moreover, no studies examine contextual influences on system-wide Lean implementation efforts in primary care. The aim of this study was to identify contextual factors most critical to implementing and scaling Lean redesigns across all primary care clinics in a large, ambulatory care delivery system. Over 100 interviews and focus groups were conducted with frontline physicians, clinical staff, and operational leaders. Data analysis was guided by a modified Consolidated Framework for Implementation Research (CFIR), a popular implementation science framework. On the basis of expert recommendations, the modified framework targets factors influencing the implementation of process redesigns. This modified framework, the CFIR-PR, informed our identification of contextual factors that most impacted Lean acceptance among frontline physicians and staff. Several domains identified by the CFIR-PR were critical to acceptance of Lean redesigns. Regarding the implementation process acceptance was influenced by time and intensity of exposure to changes, "top-down" versus "bottom-up" implementation styles, and degrees of employee engagement in developing new workflows. Important factors in the inner setting were the clinic's culture and style of leadership, along with availability of information about Lean's effectiveness. Last, implementation efforts were impacted by individual and team characteristics regarding changed work roles and related issues of professional identity, authority, and autonomy. This study underscores the need for change leaders to consider the contextual factors that surround efforts to implement Lean in primary care. As Lean redesigns are scaled across a system, special attention is warranted with respect to the implementation approach, internal clinic setting, and implications for professional roles and identities of physicians and staff.