Despite robust evidence to guide clinical care, most patients with diabetes do not meet all goals of risk factor control. Improved patient-provider communication during time-limited primary care visits may represent one strategy for improving diabetes care. We designed a controlled, cluster-randomized, multi-site intervention (Pre-Visit Prioritization for Complex Patients with Diabetes) that enables patients with poorly controlled type 2 diabetes to identify their top priorities prior to a scheduled visit and sends these priorities to the primary care physician progress note in the electronic medical record. In this paper, we describe strategies to address challenges to implementing our health IT-based intervention study within a large health care system. This study is being conducted in 30 primary care practices within a large integrated care delivery system in Northern California. Over a 12-week period (3/1/2015-6/6/2015), 146 primary care physicians consented to enroll in the study (90.1%) and approved contact with 2496 of their patients (97.6%). Implementation challenges included: (1) navigating research vs. quality improvement requirements; (2) addressing informed consent considerations; and (3) introducing a new clinical tool into a highly time-constrained workflow. Strategies for successfully initiating this study included engagement with institutional leaders, Institutional Review Board members, and clinical stakeholders at multiple stages both before and after notice of Federal funding; flexibility by the research team in study design; and strong support from institutional leadership for “self-learning health system” research. By paying careful attention to identifying and collaborating with a wide range of key clinical stakeholders, we have shown that researchers embedded within a learning care system can successfully apply rigorous clinical trial methods to test new care innovations.