The case for research to promote equity in health in resource poor contexts such as Malawi is compelling. In Malawi, nearly half of all the people with tuberculosis cannot afford to access free tuberculosis services. In this scenario, there is a clear need to understand the multiple barriers poor women and men face in accessing services and pilot interventions to address these in a way that engages policy makers, practitioners and communities. This paper provides a critical reflection on our experience as applied social researchers working at the REACH (Research for Equity and Community Health) Trust in Malawi. Our work largely uses qualitative research methodologies as a tool for applied social research to explore the equity dimensions of health services in the country. We argue that a key strength of qualitative research methods and analysis is the ability to bring the perceptions and experiences of marginalised groups to policy makers and practitioners. The focus of this paper is two-fold. The first focus lies in synthesising the opportunities and challenges we have encountered in promoting the use of applied social research, and in particular qualitative research methods, on TB and HIV in Malawi. The second focus is on documenting and reflecting on our experiences of using applied social research to promote gender equity in TB/HIV policy and practice in Malawi. In this paper, we reflect on the strategic frameworks we have used in the Malawian context to try and bring the voices of poor women and men to policy makers and practitioners and hence intensify the research to policy and practice interface.