The objective of our work was to investigate innovative sustainable cropping systems to produce regular yields of wheat with a satisfactory grain protein concentration in organic farming systems. Achieving good production levels in stockless French organic farming systems is a major challenge due to strong N limitation. Our approach is mainly based on a better valorisation of the natural nitrogen resources from soil mineralisation and symbiotic fixation of legumes, and not by an increase in the use of organic fertiliser. Two experiments were carried out in southwestern France where winter wheat and durum wheat were grown for their use in human consumption (bread and pasta, respectively). On one hand, cover crops were sown in summer and were incorporated in early November just before the wheat was sown. On the other hand, wheat was cultivated in mixture (intercropping) with a grain legume such as winter pea or fababean. The cover crops were found to be effective in the case of rainy winter years i) because of their role as a nitrate catch crop to mitigate nitrate leaching and ii) because they made it possible to increase the yield and the protein concentration of wheat grains by increasing available N (role of green manure). In the case of intercropping, wheat yield was reduced in comparison to a wheat crop alone, as expected, but the protein concentration was significantly increased and the whole grain yield (wheat + legume) was increased. Thus, in organic farming, intercrops seem to be more effective for enhancing natural nitrogen resources. However, it is still necessary: (i) to optimise the technical sequences of these two farming systems, and; ii) to determine the role of intercrops within rotations and to analyse their effect for both pests and diseases management, which is crucial in organic farming systems.