Regulatory science has been reframed for evaluating environmental risks of GM crops in both the USA and Europe. Social conflict has contributed to disputes over scientific evidence and thus increased scientific uncertainty. Environmentalist criticisms have influenced mainstream debates about how to define harm, how to evaluate GM crops vis-à-vis alternatives, and how to design risk research. Regulatory criteria have been reconstructed through socio-cultural values, public protest and institutional responses. Regulatory changes can be understood as four related processes. New scientific uncertainties have arisen from public-scientific debate. Extra-scientific judgements have been acknowledged within regulatory issues and expert advice, rather than remain hidden behind ‘science’. Criteria for evidence of safety have become more stringent, specifically regarding environmental norms and causal pathways of potential harm. Trans-Atlantic trade conflicts have been a source of political opportunities and scientific resources for those regulatory changes, especially in the US.