To derive evidence-based and stakeholder-informed research priorities for implementation in African settings, the international research consortium Collaboration for Evidence-Based Healthcare and Public Health in Africa (CEBHA+) developed and applied a pragmatic approach. First, an online survey and face-to-face consultation between CEBHA+ partners and policy-makers generated priority research areas. Second, evidence maps for these priority research areas identified gaps and related priority research questions. Finally, study protocols were developed for inclusion within a grant proposal. Policy and practice representatives were involved throughout the process. Tuberculosis, diabetes, hypertension and road traffic injuries were selected as priority research areas. Evidence maps covered screening and models of care for diabetes and hypertension, population-level prevention of diabetes and hypertension and their risk factors, and prevention and management of road traffic injuries. Analysis of these maps yielded three priority research questions on hypertension and diabetes and one on road traffic injuries. The four resulting study protocols employ a broad range of primary and secondary research methods; a fifth promotes an integrated methodological approach across all research activities. The CEBHA+ approach, in particular evidence mapping, helped to formulate research questions and study protocols that would be owned by African partners, fill gaps in the evidence base, address policy and practice needs and be feasible given the existing research infrastructure and expertise. The consortium believes that the continuous involvement of decision-makers throughout the research process is an important means of ensuring that studies are relevant to the African context and that findings are rapidly implemented.