Designing innovative combinations of techniques to improve the sustainability of cropping systems in poor countries is a major challenge. Here, we developed a prototyping methodology to design, assess and adapt a crop management system for a specific set of constraints. It was applied in Mali with the aim of designing innovative prototypes of cotton management systems to be further tested and adapted by farmers. The prototype aimed at shortening the cotton cycle to overlap the rainy season. The prototype is particularly suited for late sowing and for regions where rainfall is often insufficient.We propose a conceptual model that organizes technical interventions to shorten the cotton cycle. We developed a set of indicators to evaluate the relevance of each modified technical intervention, by comparison with current farmer practices. We evaluated the overall performances of the prototype by taking into account economic, environmental and social factors. The prototype was tested and adjusted in six trials between 2002 and 2004. Our results show that the cotton growth cycle was reduced by 15 days on average, mainly through the shortening of the flowering period. The combination of much higher stand density than currently applied in the region and application of the growth regulator mepiquat chloride produced a much higher number of bolls per hectare of +69%. The prototype produced higher seed-cotton yields, of +44% on average, and much higher gross margin than the standard cotton management system. The method was therefore successful in designing a new cotton management system that helps farmers to adapt to diverse cropping conditions.