This article analyzes the reasons why in 2010 the European Commission proposed a legislative framework on genetically modified organisms (GMOs) that could give some powers back to the Member States. This legislative proposal is puzzling since it moves the centre of decision‐making regarding the cultivation of GMOs from the EU level back to the domestic level and it also contradicts the generally acknowledged behaviour of the Commission as a competence maximizer. Using a multilevel governance perspective and based on an extensive literature review and semi‐structured interviews, the article examines the dynamics and relationships between the various levels of governance that generated pressures on the Commission to issue this counterintuitive proposal. The findings suggest that the Commission is making a (necessary) trade‐off between, on the one hand, the respect of international obligations and the preservation of the internal market, and on the other hand, internal pressures towards stricter regulation of GMOs.