Despite long histories of traditional food security, Indigenous peoples globally are disproportionately exposed to food insecurity. Addressing this imbalance must be a partnership led by Indigenous peoples in accordance with the UN Declaration of the Rights of Indigenous Peoples. We report the co-design process and resulting design of a food security research project in remote Australia and examine how the co-design process considered Indigenous peoples’ ways of knowing, being, and doing using the CREATE Tool. Informed by the Research for Impact Tool, together Aboriginal Community Controlled Health Organisation staff, Indigenous and non-Indigenous public health researchers designed the project from 2018–2019, over a series of workshops and through the establishment of research advisory groups. The resulting Remote Food Security Project includes two phases. Phase 1 determines the impact of a healthy food price discount strategy on the diet quality of women and children, and the experience of food (in)security in remote communities in Australia. In Phase 2, community members propose solutions to improve food security and develop a translation plan. Examination with the CREATE Tool showed that employing a co-design process guided by a best practice tool has resulted in a research design that responds to calls for food security in remote Indigenous communities in Australia. The design takes a strengths-based approach consistent with a human rights, social justice, and broader empowerment agenda. Trial registration: The trial included in Phase 1 of this project has been registered with Australian New Zealand Clinical Trials Registry: ACTRN12621000640808.