In this research project, we develop and apply an interdisciplinary framework for assessing and comparing environmental, economic, and social sustainability of cotton production in Sub-Saharan Africa. Our analysis includes several currently practiced organic and conventional ways of cotton production as well as some innovative—potentially more sustainable—ways of cotton production. Sustainability is assessed by several indicators, e.g. pesticide residues, soil fertility, greenhouse gas emissions, competitiveness, income and employment generation, and social conditions along the value chains. The empirical studies are conducted in Benin and Tanzania, representing West and East Africa, respectively.