It is becoming increasingly important for researchers to critically reflect on approaches that can have a positive impact on the health outcomes of indigenous people. Such issues are of great importance and perhaps of special relevance to researchers in the Global South, and to the African context in which we work.To share some lessons learned from our fieldwork to contribute to current knowledge and conversations on decolonising research process.We used an African lens to critically reflect upon some issues raised from individual interviews and focus group discussions with our participants which we deem to be important for consideration in a decolonising research process.The major issues that we raise are about important structures such as power, trust, cultural competence, respectful and legitimate research practice and recognition of individual and communities' health assets in a decolonising research process.Our paper argues for alternative approaches which are culturally appropriate for health research and for improved health outcomes of marginalised groups. In addition, we argue that participatory and transformative research methods which recognises individual and communities' assets are needed. We hope that the lessons that we share in this paper can contribute towards a respectful and good research practice among the marginalised population groups in our context.