The cultivation of genetically modified (GM) crops in the European Union (EU) is highly harmonised, but with persisting conflicts over authority. The European Commission responded to internal and external pressures with a more flexible approach to coexistence, a proposed opt-out clause, and a promise to review the existing EU GM regime, providing an opportunity to consider and suggest paths of development. This article considers the post-authorisation policy-making powers of Member States and subnational regions, in light of subsidiarity-based multilevel governance. It considers the different approaches to risk-centred issues and more general policy choices. Overall, the developments occurring at the EU level are strengthening subsidiarity-based multilevel governance within the GM cultivation regime, but with significant opportunities to improve it further through focussing particularly on the complementary powers, coordination and the regional levels.