Over the past decade, the Mediterranean maritime space has become increasingly securitised, as the humanitarian objective of saving lives of those in distress at sea has been subordinated to the objective of protecting European borders. Amid the coronavirus outbreak in 2020, states (like Italy and Malta) have introduced ‘quarantine ships’ for the transfer of rescued migrants at sea upon declaring that their ports were no longer ‘safe’ for migrant arrivals. In this regard, the right to liberty and security, as found in Article 5 of the European Convention on Human Rights (ECHR), allows under paragraph 1(e) the deprivation of liberty and the lawful detention of persons by virtue of preventing the spread of infectious diseases. Accordingly, the European Court of Human Rights (ECtHR, the Court) will often assess the manner and method of execution of the detention in conjunction with Article 3 of the ECHR in order to provide adequate safeguards against the risk of ill-treatment during such deprivation. This contribution aims to critically assess the impact and lawfulness of the measures adopted during the COVID-19 pandemic against the human rights of migrants rescued at sea. Against this background, it ponders the following question: are the ‘special’ quarantine measures – the use of quarantine ships – adopted by Italy and Malta in respect of migrants rescued at sea in accordance with existing criteria for the lawful deprivation of liberty? It is posited that the answer lies in evaluating these practices in light of human rights principles at stake as well as examining the jurisprudence of the ECtHR in light of similar issues concerning the prevention of the spread of infectious diseases. In this way, the pandemic angle becomes central to this analysis, underlining the need to advance human rights principles together with the rule of law. The contribution maintains that from a human rights perspective, quarantining migrants offshore is problematic, as the practice involves detaining persons at sea, precisely after a traumatic and perilous sea journey, without considering that a large number of them have escaped persecution, violence and other atrocious conditions. In conclusion, these practices might give rise to other potential human rights violations, including Article 2 and Article 3 of the ECHR.