In the European Union, the separation of genetically modified (GM) and non-GM food supply chains, from fields to country elevators, is a major constraint on the coexistence of these two sectors, providing “freedom of choice” for both farmers and consumers. Both technical aspects, focusing on risks of admixture due to gene flow and the organisational challenges faced by stakeholders must be taken into account. We combined role-playing games with the use of gene flow simulators operating at the landscape level to determine how farmers, elevator companies and technical advisers could manage coexistence for oilseed rape crops in Beauce (France) and maize in Alsace (France). The games highlighted the importance of access to information, co-ordination and learning processes. The results were summarised as five contrasting scenarios, defined in terms of the stakeholders’ management ability and the structural risks of admixture between GM and non-GM material. These results raise questions about the links between the rigidity of regulation and the diversity of the strategies used by stakeholders to manage grain and oilseed quality.