The European Union (EU) is currently facing a challenge that might unnecessarily hamper the adoption of GM crops: regulating the coexistence of genetically modified (GM) and non-GM crops. Member states are currently implementing or developing both ex ante coexistence regulations and ex post liability schemes to ensure that both GM and non-GM crops can be cultivated in the EU. In this article, we explore in detail how national and/or regional policymakers can build in a certain degree of flexibility in ex ante coexistence regulations in order to reduce the regulatory burden on certain agricultural options and avoid jeopardising the economic incentives for coexistence. We use the example of GM maize as a case study, being the only GM crop planted over a significant area in the EU. We conclude that flexibility could be integrated into regulations at different levels: (i) at the regulatory level by relaxing some of the regulatory rigidity in ex ante regulations; (ii) at the farm level by allowing the substitution of isolation distances by pollen barriers; and (iii) at the national/regional level through plural coexistence measures, consistent with heterogeneity of farming in the EU.