Responding to mistrust in the European agencies’ risk assessments in politically salient cases, the European Union (EU) legislator, the European Food Safety Authority and the European Medicines Agency alike have accelerated their efforts to foster EU regulatory science transparency. These simultaneous endeavours have, however, taken place in a fragmented legislative and administrative context, with each agency operating under a different legal framework. By focusing on authorisation procedures, from registration of studies to authorisation of novel foods, pesticides and human medicines, this article examines the resulting regimes governing the disclosure of scientific data by EU agencies to identify common trends and sectoral specificities. Against the background of an overall shift towards enhanced transparency, we shed light on, first, the circulation of institutional arrangements and practices among agencies and, second, the new dimensions of transparency emerging from these developments. We also highlight the remaining sectoral differences and argue that they could have potentially large impacts on the amount and type of information disclosed and on the level of transparency perceived by stakeholders and citizens. We argue that more coherence across the sectoral transparency regimes is needed, in particular in light of the agencies’ contested legitimacy and of their increasing cooperation on cross-cutting issues like antimicrobial resistance and medicine and pesticide residues in food.