The Primary Care Capacity Project (PCCP), implemented by the Louisiana Public Health Institute, systematically and rigorously applied qualitative methodologies beyond simple interviews and focus groups to develop the project areas of focus, evaluate clinical transformation interventions in selected heath centers along the Gulf Coast, and provide data and support to foster ongoing quality improvement approaches. Qualitative methodologies were utilized for formative, implementation, and summative evaluation. During the early formative stages of PCCP, community prioritization meetings were conducted in Louisiana, Mississippi, Alabama, and Florida, in which key stakeholders were asked to brainstorm and prioritize major health issues and recommendations in their communities. Findings from these meetings were then used to inform PCCP clinic funding and other community priorities. During project implementation, dyadic interviews were facilitated around specific PCCP areas of focus. These dyadic interviews were valuable in that they uncovered stories, successes, and challenges of clinical transformation. Moreover, they promoted peer-to-peer learning among diverse health centers. The relationships between interview participants are likely to continue past the grant period and further promote innovation and efficiency. Finally case studies were conducted to inform actionable recommendations tailored to each health center. These data also provided value add back to the health centers as they used the information to guide programming and quality improvement efforts. Qualitative methods are critical tools for public health practitioners to support project planning and improvement as well as community change.