Past interventions and proposed technologies have often failed to alleviate problems of soil fertility and food production in sub-Saharan Africa as they are delivered as single component solutions that rarely address the complexity of the livelihoods of farmers. Further agricultural intensification is often addressed in isolation from the effects that it may have on the wider environment and on ecosystem services of importance at regional and global scales. A series of databases and an analytical modelling framework, AfricaNUANCES that combines spatial and temporal dimensions of African smallholder farming systems will be developed. A primary aim is to synthesize knowledge and analyse tradeoffs of implementing various soil fertility technologies for smallholder farmers in mixed crop/livestock systems in East, West and Southern Africa. Emphasis will be on efficiency of targeting and use of nutrients and legume-based soil improving technologies, with outputs evaluated in terms of costs, benefits and compromises in productivity, economics and environmental services. Our approach is to aim for simplicity to allow wide access and use of the AfricaNUANCES framework, whilst encouraging deeper systems analysis around questions that require trade-offs between individual goals and those of society at large.