Pests, diseases and weeds are major constraints to cropping system intensification in sub-Saharan Africa. Four major intensification systems to achieve sustainable agriculture have been identified: conventional with high input, organic, agroecological and eco-technical 'sustainable intensive'. Those systems display advanced crop protection. Here we review the performance of those systems in the context of sub-Saharan Africa. The major points are: (1) Unlike economies of Europe and North America following World War 2, and of Asia and Latin America following the Green Revolution, sub-Saharan Africa rural economies were not transformed by conventional intensification involving cultivation of cash crops for export and over-reliance on pesticides. Genetically modified crops were used only to a limited extent at the regional level. (2) Most staple food-based cropping systems are de facto organic due to the unavailability of synthetic inputs. Organic systems are thus developing for some export cash crop sectors, with synthetic pesticides are being substituted by non-chemical pesticides. (3) Agroecological crop protection focuses on biological pest regulations such as the replacement of chemical inputs, thus implying the re-design of cropping systems. (4) For crop protection, the eco-technical pathway, which is based on principles of integrated pest management and ecological intensification, is more flexible and pragmatic than the other systems. In this review we compare the different systems, notably their contribution to six ecosystem services connected with crop protection issues: biomass production, pest and disease regulation, maintenance of water quality, biodiversity conservation, pollination and climate change mitigation. We then identify research needs in the context of food security, urbanization, trade globalization and climate change.