Regulatory decision-making over the use of products of new technology aims to be based on science-based risk assessment. In some jurisdictions, decision-making about the cultivation of genetically modified (GM) plants is blocked supposedly because of scientific uncertainty about risks to the environment. However, disagreement about the acceptability of risks is primarily a dispute over normative values, which is not resolvable through natural sciences. Natural sciences may improve the quality and relevance of the scientific information used to support environmental risk assessments and make scientific uncertainties explicit, but offer little to resolve differences about values. Decisions about cultivating GM plants will thus not necessarily be eased by performing more research to reduce scientific uncertainty in environmental risk assessments, but by clarifying the debate over values. We suggest several approaches to reveal values in decision-making: (1) clarifying policy objectives; (2) determining what constitutes environmental harm; (3) making explicit the factual and normative premises on which risk assessments are based; (4) better demarcating environmental risk assessment studies from ecological research; (5) weighing the potential for environmental benefits (i.e., opportunities) as well as the potential for environmental harms (i.e., risks); and (6) expanding participation in the risk governance of GM plants. Recognising and openly debating differences about values will not remove controversy about the cultivation of GM plants. However, by revealing what is truly in dispute, debates about values will clarify decision-making criteria.