The integration of crops and animals is an option to reduce mineral fertiliser use through the recycling of nutrients in animal manure on croplands. But the increasing specialisation and spatial segregation of crop and livestock production systems both at the farm and the district scale may hamper the proper recycling of nutrients between these two activities. However, the effect of such segregation has only been investigated on some case-studies – mostly at the regional and the local scale – while we still lack of systematic assessment of this segregation in terms of mineral fertiliser use on a range of scales. In this paper, we estimated the effect of this segregation on nutrient resource use at the district scale. Phosphorus (P) fertiliser was considered since it is produced from a finite resource that needs to be more efficiently recycled in agriculture and France was chosen as a case study, representative of industrial countries with a wide range of variations in crop and livestock segregation. We quantified the effect of livestock density on mineral P fertiliser use and the effect of crop and livestock spatial segregation on P fertiliser use and its substitution with P in animal manure. Our results showed that P fertiliser use decreased with increasing livestock density at the district scale. However, the substitution of P fertiliser with P in animal manure was only partial (probably due to more N- than P-oriented decision making by farmers and low N:P ratio of organic manure), leading to large nutrient surpluses in districts with high livestock densities (>1.1 livestock unit per agricultural area). Finally, P fertiliser use increased with the spatial segregation of crops and livestock. Overall, our results demonstrated that lower segregation of crops and animals could help to save non-renewable resources, and that improvements in manure management are required.