In rural Native American communities, access to healthy foods is limited and diet-related disparities are significant. Tribally owned and operated convenience stores, small food stores that sell ready-to-eat foods and snacks primarily high in fat and sugar, serve as the primary and, in some areas, the only food stores. The Tribal Health and Resilience in Vulnerable Environments or "THRIVE" study, implemented between 2013 and 2018, is the first healthy retail intervention study implemented in tribally owned and operated convenience stores. THRIVE aims to increase vegetable and fruit intake among Native Americans living within the Chickasaw and Choctaw Nation of Oklahoma. The study comprises three phases: 1) formative research assessing tribal community food environments and associated health outcomes; 2) intervention development to assess convenience stores and tailor healthy retail product, pricing, promotion, and placement strategies; and 3) intervention implementation and evaluation. In this paper we share the participatory research process employed by our tribal-university partnership to develop this healthy retail intervention within the unique contexts of tribal convenience stores. We summarize our methods to engage tribal leaders across diverse health, government, and commerce sectors and adapt and localize intervention strategies that test the ability of tribal nations to increase fruit and vegetable purchasing and consumption among tribal members. Study processes will assist in developing a literature base for policy and environmental strategies that intervene broadly to improve Native community food environments and eliminate diet-related disparities among Native Americans.