Background Indigenous academics advocate for the integration of indigenous methodologies in research involving ATSI people. Implications of how to integrate these models are not well understood. This scoping review is intended to shed light on different ATSI research methodologies and how they can be applied in health research. Method A literature search was performed of PubMed, Lowitja Institute LitSearch and CINAHL from 2010 to 2024. Results The AIATSIS (Australian Institute for ATSI Studies) Code of Ethics published in 2020 is a critically important document that outlines the principles by which ATSI research should be approached. It is centered around integrity, achieved through indigenous leadership, sustainability, accountability, and indigenous self determination. Aboriginal Participatory Action Research (APAR) is the overarching guideline to ensure participants are also active contributors. Other recurring methodologies included storytelling, yarning and western methods within general indigenous frameworks. These methodologies prioritise the importance of consultation, collaboration, and the involvement of Indigenous voices at every stage to ensure alignment with traditional knowledge systems that have existed for thousands of years. Conclusion Research involving ATSI populations should be undertaken while ensuring ethical integrity, respect for self-determination, and sustainability. Yarning method, requires clearer definitions in the literature to promote consistency and provide future researchers with the necessary tools to conduct responsible research that respects cultural perspective and tradition. This approach fosters more relevant and sustainable outcomes for Indigenous communities.