New organic cropping systems are needed to keep pace with the growing demand for organic food. Those systems should ideally give more yield and safe for the environment. Current innovations such as non-inversion tillage with cover crops are promising, but investigations usually do not take farmers view into account. Therefore, research work should include farmer participation to maximize success. We present here a method to help farmers in designing innovative cropping systems. This method involves several design workshops with farmers. The first steps of the method foster creativity by changing ways in which farmers thought and worked. The final steps of the method facilitated learning. Participatory tools are used to exchange views and knowledge. System prototypes were developed. The method was applied using groups of six and seven farmers from two French regions. The farmers generated 14 system prototypes. We found that system prototypes differed radically from current practices because prototypes are based on biological rather than mechanical methods. Indeed, cover crop use was almost four times more frequent in prototypes than in current systems. Moldboard plowing and mechanical weeding frequencies were, respectively, two and eight times lower. The main benefits of our method are (1) the involvement of volunteer farmers in the design process, (2) the combination of farmer knowledge and scientific knowledge, and (3) the use of various methodological supports.