Background: Despite increasing investment in health research capacity strengthening efforts in low and middle income countries, published evidence to guide the systematic design and monitoring of such interventions is very limited. Systematic processes are important to underpin capacity strengthening interventions because they provide stepwise guidance and allow for continual improvement. Our objective here was to use evidence to inform the design of a replicable but flexible process to guide health research capacity strengthening that could be customized for different contexts, and to provide a framework for planning, collecting information, making decisions, and improving performance. Methods: We used peer-reviewed and grey literature to develop a five-step pathway for designing and evaluating health research capacity strengthening programmes, tested in a variety of contexts in Africa. The five steps are: i) defining the goal of the capacity strengthening effort, ii) describing the optimal capacity needed to achieve the goal, iii) determining the existing capacity gaps compared to the optimum, iv) devising an action plan to fill the gaps and associated indicators of change, and v) adapting the plan and indicators as the programme matures. Our paper describes three contrasting case studies of organisational research capacity strengthening to illustrate how our five-step approach works in practice. Results: Our five-step pathway starts with a clear goal and objectives, making explicit the capacity required to achieve the goal. Strategies for promoting sustainability are agreed with partners and incorporated from the outset. Our pathway for designing capacity strengthening programmes focuses not only on technical, managerial, and financial processes within organisations, but also on the individuals within organisations and the wider system within which organisations are coordinated, financed, and managed. Conclusions: Our five-step approach is flexible enough to generate and utilise ongoing learning. We have tested and critiqued our approach in a variety of organisational settings in the health sector in sub-Saharan Africa, but it needs to be applied and evaluated in other sectors and continents to determine the extent of transferability. © 2014 Bates et al.; licensee BioMed Central Ltd.