A Masterclass Program was developed to strengthen the research capacity of staff within Aboriginal Community-Controlled Health Organisations (ACCHOs) and featured three Masterclasses delivered across Australia, including Understanding Research, Undertaking Research and Research Evaluation. A mixed-method process and impact evaluation of the Masterclass Program was undertaken. The process evaluation examined the reach of the Program and the impact evaluation comprised an online survey (n = 45) and semi-structured interviews (n = 21) with Masterclass participants. During 2014-17, 27 Masterclasses were delivered to 260 people, including predominantly ACCHO personnel but also Indigenous doctors and research institute staff who work closely with the ACCHO sector. Most survey respondents felt the Masterclasses improved their understanding of research and their willingness to participate in and undertake research. The qualitative analysis confirmed this and suggested that Masterclasses were implemented in a supportive learning environment which led to increased research capacity (increased research awareness, changed perceptions, increased understanding, critical thinking and new confidence) and ultimately enhanced research engagement (willingness to participate, motivating others, empowered critique of research partners and proposals, interest in further research training). Barriers to research engagement and areas for improvement of the Masterclass Program before, during and after Masterclasses were also identified.