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In order to achieve sustainable development outcomes in sub-Saharan Africa (SSA), African institutions must be the leading experts on and primary providers of research solutions to local problems. Despite years of investment in capacity building, SSA lags behind every other region in terms of research outputs and government investments, and new models for building institutional capacity are needed. Through interviews with African institutional leaders and development partners working in SSA, this study finds that funding inefficiencies lead to key challenges within institutions’ governance and management structures, financial systems, talent management processes, leadership and institutional vision capacities, and peer support networks, all of which obstruct the ability of African institutions to become impactful and sustainable drivers of development outcomes in the region. We present for consideration three possible innovative models that can facilitate the emergence of strong Africa-based, Africa-led institutions: a multi-stakeholder funding platform, an integrator organization model, and a scale model.