Recent health and environmental crises have emphasized the importance of transparency of agency science, i.e. the scientific information that underpins public regulation. Yet how EU law shapes the transparency of EU agency science and whether it contributes to publicly holding experts to account for the quality of their advice, remains an open question. This article analyses the transparency regimes of three EU agencies.We show that the EU legal approach to transparency of agency science is undergoing significant change, through legislative reform and agency practice. The traditional “passive” approach based on the Access Regulation is fragmented and reveals several shortcomings. Recent trends, such as the 2021 reform of the General Food Law, indicate that the EU is moving towards “proactive transparency”, which improves expert accountability. Our study contributes to debates on EU risk regulation and the general reform of the Access Regulation. The article offers an interdisciplinary perspective informed by political epistemology, namely the study of the role of experts in public decision-making.