For many years, we have seen an increasing specialization of agricultural systems and territories, with a clear separation between territories with very high animal densities and those devoted to the growing of annual crops. This development is explained by market and sector economic logic and has been reinforced by the availability of low-cost inputs and animal housing systems based on direct grazing not requiring straw. It has, however, also involved negative environmental impacts and, in some cases, the impoverishment of soil fertility, a loss of biodiversity, and excesses of N and P, leading to eutrophication and hot spots of ammonia emission in livestock-breeding territories. Having recapped the mechanisms behind the specialization of systems and territories, we examined the extent to which the development of innovative mixed-farming systems that reconnect livestock and crop production on various territorial scales (farm, district, region) can reduce the negative impacts of agriculture on the environment, produce valuable ecosystem services and achieve acceptable economic efficiency for farming enterprises. Examples from temperate regions will be used to show that mixed-farming systems increase the possibilities of better recycling of nutrients within systems, limiting recourse to the purchase of increasingly expensive inputs and safeguarding the biodiversity of agricultural ecosystems.