Organic agriculture could achieve the objectives of sustainable agriculture by banning the use of synthetic fertilizers and pesticides. However, organic crops generally show lower performances than conventional ones. In France, organic winter wheat production is characterized by low grain protein content. There is a crucial need for better understanding the variability of grain protein content, because millers require batches with values over 10.5% of dry matter. Here, a regional agronomic diagnosis was carried out to identify the limiting factors and crop management practices explaining the variability of grain protein content. The studied field network was a set of 51 organic winter wheat plots in south-eastern France. The mixed-model method was used for identifying and ranking the limiting factors and the crop management practices responsible for variation in limiting factors. Our results show that the grain protein content variation was mostly explained by the baking quality grade of the cultivar, crop nitrogen status and weed density at flowering. There was a positive correlation between grain protein content and both crop nitrogen status and weed density. To a lesser extent, climatic factors also explained grain protein content variability. A lower water stress increased grain protein content, whereas an increase in the photothermal quotient and daily temperature over 25 °C reduced grain protein content. In south-eastern France, grain protein content of organic winter wheat could be increased by improving fertilization management, using an improved baking quality grade cultivar, choosing a legume fodder crop as preceding crop, or by avoiding late sowing dates.