In recent years, the continuous structural change in the value chain of modern food production has been characterised by an increasing international division of labour among manufacturing companies. A regional specialisation of primary agricultural production is especially apparent in meat production. Thus, the German–Dutch border area has developed into a region of unprecedented intensive pork production. While The Netherlands specialises in piglet production, the production of fattened pigs continues to grow in northwest Germany. As a result of this increasing transnational value chain development, German imports of Dutch piglets have risen continuously since 2000. However, this structural interweaving of pork production between The Netherlands and Germany has resulted in many new challenges for the cooperation between the various participants and in particular for the administrative authorities in the field of food and feed safety as well as efficient animal disease control. The motivation for this exploratory study stems from the lack of scientific work on this topic to date. The aim of this research is to illustrate the relevance of functioning cross-border cooperation in the food sector, using commodity flow structures and disease spread analysis. Results indicate that cross-border cooperation between authorities during a CSF epidemic can reduce the risk of recurrence and the duration by 50%.