In 2011, a Belgian field trial with genetically modified crops triggered fierce public protests and debates. Opponents of the trial protested against its performance and some advocated its destruction, in response to which scientists and the government defended a scientific freedom to perform the trial. This article investigates why the different stakeholders came to occupy such mutually exclusive positions towards the trial. Based on analyses of qualitative interviews with key stakeholders, document analyses, and field observations, the article argues that the different stakeholders were involved in an ontological politics. This politics centred on the question of which ontologically different, co‐existing versions of the trial should be attended to in institutionalised scientific and political appraisals of the trial. The article concludes that the institutional handling of the trial as if it represented a single reality that merited only epistemological struggles contributed to turning a multifaceted debate into a dichotomous one, figuring field trial proponents and opponents. As such, the opposition between the different stakeholders was not antecedent to the institutional handling of the trial – as different stakeholders claimed – but rather an outcome of it.