Organic inputs in Africa are used mainly as sources of crop nutrients but most of the ones available on the farms such as crop residues, animal manures and composts are of low quality and insufficient quantity. Proper management of such organic inputs to ensure sustained crop productivity poses a major challenge. Current research efforts aim to increase the understanding of the interactions between organic inputs, the soil and the crop with a view to developing predictive management guidelines. The factors influencing nitrogen mineralization in various plant residues have been identified and a decision support system (DSS) which makes practical recommendations for their appropriate use as nitrogen sources has subsequently been developed. This DSS has, however, not proved useful when applied to animal manures. To increase nutrient use efficiency, synchronization of nutrient release from the organic materials with crop demand has been attempted but attainment of perfect synchrony appears unlikely. Given that neither organic nor inorganic fertilizers alone can achieve sustainable crop productivity, focus has now shifted to the integrated soil fertility management paradigm that advocates for combined use of organic and inorganic sources of nutrients. Whereas the biophysical aspects of organic input management have been studied in detail, social and economic analyses are rare. Our knowledge of organic input systems, therefore, remains imprecise. This has made development of economically and socially acceptable guidelines for organic input management difficult. Adoption of the organic input technologies is consequently disappointingly low and the biggest challenge is to have these technologies adopted by farmers.