Many hypotheses have been advanced to explain the collective irrationality of COVID-19 vaccine hesitancy, such as partisanship and ideology, exposure to misinformation and conspiracy theories or the effectiveness of public messaging. This paper presents a complementary explanation to epistemic accounts of collective irrationality, focusing on the moral reasons underlying people’s decisions regarding vaccination. We argue that the moralization of COVID-19 risk mitigation measures contributed to the polarization of groups along moral values, which ultimately led to the emergence of collective irrational behaviors. Collective irrationality arises from groups explicitly or implicitly endorsing values that ultimately harm both themselves and those around. The role of social media platforms in amplifying this polarization and contributing to the emergence of collective irrationality is also examined. Finally, potential strategies for addressing the moral sources of collective irrationality are discussed.