We present a quantitative description of the N and P flows characterizing the agro-food system metabolism of 33 agricultural regions in France and their time evolution since the middle of the 19th century. The data were interpreted in terms of connection between crop production, livestock breeding, human nutrition and trade of agricultural goods, and were linked to their historical background. Until the early 20th century, the integrated crop and livestock farming model dominated everywhere, and the slow increase in crop production was only possible because of an increase in livestock density. Specialized cash crop farming systems appeared in the central Paris basin only in the first half of the 20th century together with the increase in the use of industrial fertilizers. Only after WWll, under the pressure of strong interventionist policies, did specialization of French territories lead to five types of systems, favoring their openness and integration into the international market, with harmful environmental impacts. The 1980s were marked by a policy shift towards more liberalism, which reinforced specialization. However, greater environmental concern stabilized or decreased nutrient losses, while maintaining largely open biogeochemical cycles.