Abstract Background Diabetes in the United States has reached epidemic proportions and the people of Appalachia have been disproportionately affected by this disease. Strategies that complement standard diabetes care are critically important to mitigate the risk of complications, reduce health expenditures, and improve the quality of life of patients living in rural Appalachia. The purpose of this study was to conduct a qualitative process evaluation of a patient navigation program for diabetes after its first year of implementation. Methods The process evaluation assessed how the Diabetes Navigation Program was delivered as well as how it was experienced by the navigators, providers, health administrators, and office staff at an endocrine specialty center in rural Appalachian Ohio. We employed total population sampling to conduct in-depth, face-to-face interviews with all providers, health administrators, staff, and navigators at a Diabetes Endocrine Center. Interviews were transcribed, coded, and analyzed via content and thematic analyses using NVivo 11 software. Results Seventeen individuals (providers n = 5, health administrators n = 4, office staff members n = 3, and navigators n = 5) participated in in-depth, face-to-face interviews (age = 44.7 ± 11.6 years, 82.4% female, 94.1% white, 13.3 ± 9.6 years work experience). Fidelity of implementation: The navigation team carried out most of the activities denoted in the Work Plan, therefore the program was implemented somewhat successfully. Qualitative analysis revealed three themes: 1) The navigator addresses sources of health disparities: All participants described the role of the diabetes navigator as someone who is knowledgeable about diabetes and able to identify and address health disparities. 2) The navigators are the eyes in the community and the patients’ homes: Navigators offered providers and clinic staff a rare glimpse into the personal lives of patients, which led to the identification of unrecognized barriers. 3) Difficulties with cross-system integration of services: Differences in the organizational culture and vision of the specialty center and navigation office contributed to systemic barriers. Conclusions Overall, this process evaluation highlights the importance of coordinating providers, health administrators, medical office staff, and navigators to address barriers to diabetes care. Forthcoming research is needed to document the clinical effectiveness and sustainability of the Diabetes Navigation Program in rural Appalachia.