A growing proportion of people living with HIV/AIDS also struggle to cope with one or several noncommunicable diseases (NCDs), particularly as they age. The two epidemics being intertwined, there is increasing recognition that that there should be closer advocacy, policy and programmatic links between HIV and NCDs. The objective of this paper is to discuss the development of a research agenda geared towards informing the design and implementation of programs and policies truly grounded in a co-benefits approach. Tackling the joint epidemics of HIV/AIDS and NCDs in Africa will require for research funders and private and foreign aid donors to be bold, visionary and to commit to long-term research investments in order to evaluate the effects of natural policy experiments and complex interventions.