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Closing the gap between evidence and practice demands interventions targeting the whole practice. These system level interventions require more complex designs and require greater practice involvement. Current descriptions of trials use research designs that either limit practice involvement or make use of large health system resources.To share insights on retention of practices in a complex clinical trial aimed at improving care of multiple chronic conditions in 60 diverse community primary care practices not supported by large health system resources.Qualitative cross case analysis of field notes from meetings of a diverse research team.Five interrelated factors were found to be important to the success of the study implementation process: (1) developing structure and activities for relationship building; (2) attention to consistent communication; (3) timely information sharing; (4) evolution of a cross-functional research team; (5) provision of technical assistance. Specific strategies were identified to overcome challenges to study implementation.Diverse community primary care practices without support from health system resources will complete participation in complex trials. Researchers need not avoid answering questions requiring complex study designs; however, successful implementation requires an individualized approach tailored to the needs and characteristics of each practice.