Collaborations are vital in health research, and the need for equitable benefits, particularly in North-South collaborations, cannot be over-emphasized. Although efforts such as increased inclusion of Southern partners in agenda-setting and publications are being made to enhance equity, there have been few empirical studies on the effect of management practices on partner benefits. We therefore sought to examine management strategies adopted by consortia and their influence on partner benefits. Using a qualitative approach, we conducted a case study involving three Africa-led health research capacity strengthening consortia of the DELTAS Africa initiative. We conducted 44 in-depth interviews with consortium directors, managers, partner representatives, and other actors, and used the framework approach to analyse the data. Consortium management processes include selecting partners, determining consortia goals, assigning roles, allocating resources, instituting governance processes, and managing partners. Consortia leaders encountered tensions between diverse management strategies during these processes. For instance, leaders were torn between selecting institutions with the capacity to produce required deliverables as partners, or institutions with less capacity but who needed the consortium’s capacity strengthening opportunities. Consortia also encountered tensions between allocating resources based on need or ability to spend, a centralised or decentralised approach to partner management, and greater control or shared power in governance structures. Often, due to funder requirements, consortia tend to favour strategies that enable more efficient delivery of programme outputs. However, these strategies do not always engender the best research capacity gains and appear to promote vicious cycles of stronger partners getting stronger and less capacitated partners staying less capacitated. The study established that ‘learning by doing’ consortium management is a capacity strengthening mechanism in its own right. Thus, practices such as incorporating goals that address gaps in local research systems even when outputs cannot be measured in the short-term, and increased partner responsibilities even when it seems less efficient are valuable for enhancing partner benefits. Consortium management processes enhance partners’ capacities. Thus, management capacity should be a key goal in itself and not just a means of achieving other capacity goals. It is therefore essential to carefully plan for and resource management processes in consortia.