In this paper, we analyse some of the challenges that pharmacovigilance, the science of detecting and assessing possible adverse reactions from medical interventions, is facing during the COVID-19 pandemic. In particular, we consider the issue of increased uncertainty of the evidence and the issue of dealing with an unprecedented amount of data. After presenting the technical advances implemented in response to these two challenges, we offer some conceptual reflections around such practical changes. We argue that the COVID-19 emergency represents a chance to push forward critical thinking in the field of pharmacovigilance, and that contributions from epistemology, ethics and philosophy of science are necessary to increase resilience in the face of this and future health emergencies.