Aboriginal and Torres Strait Islander people living in remote communities in Australia experience a disproportionate burden of diet-related chronic disease. This occurs in an environment where the cost of store-purchased food is high and cash incomes are low, factors that affect both food insecurity and health outcomes. Aboriginal and Torres Strait Islander storeowners and the retailers who work with them implement local policies with the aim of improving food affordability and health outcomes. This paper describes health-promoting food pricing policies, their alignment with evidence, and the decision-making processes entailed in their development in community stores across very remote Australia. Semi-structured interviews were conducted with a purposive sample of retailers and health professionals identified through the snowball method, September 2015 to October 2016. Data were complemented through review of documents describing food pricing policies. A content analysis of the types and design of policies was undertaken, while the decision-making process was considered through a deductive, thematic analysis. Fifteen retailers and 32 health professionals providing services to stores participated. Subsidies and subsidy/price increase combinations dominated. Magnitude of price changes ranged from 5% to 25% on fruit, vegetables, bottled water, artificially sweetened and sugar sweetened carbonated beverages, and broadly used ‘healthy/essential’ and ‘unhealthy’ food classifications. Feasibility and sustainability were considered during policy development. Greater consideration of acceptability, importance, effectiveness and unintended consequences of policies guided by evidence were deemed important, as were increased involvement of Aboriginal and Torres Strait Islander storeowners and nutritionists in policy development. A range of locally developed health-promoting food pricing policies exist and partially align with research-evidence. The decision-making processes identified offer an opportunity to incorporate evidence, based on consideration of the local context.