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ABSTRACT Antimicrobial resistance (AMR) ranks among the top three health threats facing the EU. The AMR crisis is characterized as a “creeping crisis” and refers to the development where the increase in AMR causes antibiotics to lose their efficiency and effect—potentially causing millions of deaths. This article explores the EU's efforts to manage the AMR crisis by linking and coordinating different policy sectors. It assumes that institutional factors at the meso‐level, that is, at the level where political strategies are transformed into action, are key to ensure coordination across policy‐sectors and thus successful implementation of inter‐sectorial AMR policies. Drawing on literature on historical institutionalism, we analyze the development of institutional conditions for coordinating the three key sectors of AMR‐governance in the EU: the human health, veterinary, and environmental sectors. The starting point is the observation that the latter sector is considerably less integrated into AMR governance than the other two sectors. The article describes and explains how institutional developments at the meso‐level of AMR governance in the EU (European Commission Directorate‐Generals (DGs), EU agencies) contribute to an inter‐sectoral coordination deficit, or a “blind spot,” in the combat against AMR.