The Washington State Multi-Payer Medical Home Reimbursement Pilot (Pilot) tested a payment method for the patient-centered medical home (PCMH) model intended to reduce avoidable emergency department (ED) and hospitalization rates. Very little is known about the primary care clinic (clinic) experience with various payment methods designed for the medical home model. The objective was to elicit and describe the primary care clinic experience among various medical groups in Washington State's payment Pilot. This was a qualitative analysis of semi-structured interviews conducted in January 2014 to identify enabling features (or "facilitators") as well as barriers to successful implementation of PCMH in this multi-payer pilot. Participants were clinical and administrative staff of Pilot clinics representing various types of health systems under 8 parent organizations across Washington State. Pilot clinics across Washington State chose evidence-based population health strategies to achieve Pilot targets. Pilot clinics encountered more barriers than facilitators when implementing strategies. A key facilitator was having timely access to ED and hospital clinical data. A common barrier was the cost of infrastructure development to implement strategies. Other barriers included lack of data to guide interventions and insufficient payment for care management and quality improvement work. It will take more than just primary care transformation to improve health outcomes--a significant transformation in data collection, reporting and payment needs to match the change occurring in clinics.