Across the African continent efforts to intensify agriculture have been limited to specific commodities, locations or particular production schemes. The causes for the widespread failure to overcome low land and labor productivity while maintaining ecosystem services have often be analyzed but remain poorly understood. A social-ecological system approach may help to better understand the complex nature of ecological disadvantages, postcolonial structures, limited connect between producers and consumer markets, low off-farm livelihood opportunities, partial underpopulation and lacking experience with the concept of sustainable production as a major impediment for sustainable intensification of the agricultural sector. Nevertheless, recent success stories in agro-pastoral systems as well as urban vegetable and animal production and associated value chains in West Africa, and in intensive mixed-cropping systems of the Great Lakes Region show the potential of stakeholder-driven agricultural intensification. Proper interpretation of these cases may provide lessons for a more widespread eco-intensification of smallholder agriculture in sub-Saharan Africa.