In this article, we ask what the impact is of the role of the EU administration in responding to emergencies in terms of (changes to) the rule of law. A response to an emergency in some cases creates exceptions to rule of law guarantees that bind the authorities to procedural rules and fundamental rights. These exceptions can become more permanent and even change the constitutional order of the EU. We articulate the legal framework for health emergencies, and discuss how the EU court has interpreted and developed this framework in two key decisions. We then ask whether this framework offers adequate safeguards for upholding the rule of law in cases of major health emergencies. We conclude that public health emergencies can bend and even break rule of law requirements for the EU administration, and advocate for more legal guidance on proportionality, which may offer better safeguards suited for protecting the rights of affected parties.