The cultivation of genetically modified (GM) crops in the EU is highly harmonised, but with persisting conflicts over authority. The Commission responded to internal and external pressures with a more flexible approach to coexistence, a proposed optout 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 on the complementary powers, coordination and the regional levels in particular.