Alternative payment models have been proposed as a way to facilitate patient-centered medical home model implementation, yet little is known about how payment reform translates into changes in care delivery. We conducted site visits, observed operations, and conducted interviews within 3 Federally Qualified Health Center organizations that were part of Oregon's Alternative Payment Methodology demonstration project. Data were analyzed using an immersion-crystallization approach. We identified several care delivery changes during the early stages of implementation, as well as challenges associated with this new model of payment. Future research is needed to further understand the implications of these changes.