Young people who engage in multiple risky behaviours (high-risk young people), such as substance abuse, antisocial behaviour, or suicidal ideation, are more likely to experience serious harms later in life. Despite these harms, there is extraordinarily little intervention research available to guide policy makers’ or service providers’ decision making about investing in effective programs for high-risk young people (HRYP). One potential reason for this is that most interventions available for vulnerable populations globally, are implemented by NGO’s (Non-Government Organisations) that typically lack the capacity and capability to conduct rigorous evaluation in addition to their primary service delivery roles. There is also little to no consideration given to the application of Indigenous Data Sovereignty (IDS) principles in the context of generating evidence with young Indigenous peoples. This thesis presents a range of methods that could be adopted by NGOs to design and deliver evidence-based programs for HRYP, and to explore the capacity to integrate more routine monitoring and evaluation into NGO’s delivery of those programs. This thesis seeks to demonstrate how research can be grounded in principles of IDS and considers methods for how research might best be operationalised in the context of NGO-delivered programs for HRYP. It is hoped that this approach may provide an exemplar for other programs, research projects and organisations that use data from Indigenous controlled organisations and from Indigenous peoples. The implications of the findings from this thesis, and recommendations for future research and practice implementation, are discussed. Dissemination of the methods described in this thesis will not only improve the internal capacity and capability of NGO-delivered programs to conduct evaluations in collaboration with researchers but will also increase the capacity of Indigenous peoples and communities to advocate for greater sovereignty in relation to the data and research methods with which they choose to engage. These improvements will lead to better outcomes for HRYP and their communities.