Recent threats to the durability of the non-refoulement principle brought on by COVID-19 demonstrate how the pandemic has been much more than a health crisis. Public health emergency measures issued in response to the global outbreak, such as port closures, the suspension of search-and-rescue operations and privatised pushbacks at maritime borders, have exposed fundamental weaknesses in the international protection regime. With Italy and Malta in profile, this article examines how the elevation of COVID-19 to a national security threat has occasioned a shift in the migration and security discourse, challenging the very existence of the non-refoulement principle’s non-derogable character. In support of conceiving the principle as absolute, the article reviews how the denial of protections under non-refoulement has contributed to the scale and gravity of the present health crisis, forcing mixed migrant arrivals to either stay in overcrowded camps or in protracted situations of distress at sea. The article thereby concludes that the framing of migration as a health security issue appears to only breed greater insecurity.