The COVID-19 pandemic has severely disrupted non-coronavirus clinical trials. In the case of life-threatening diseases, such as cancer, this is particularly dangerous, as treatment cannot simply be stopped. In the EU, guidelines for the management of ongoing studies were issued; however, national coordination is still lacking. This article aims to raise awareness on the struggle of managing ongoing clinical trials in the EU during the pandemic. The goals are to bring attention, from a legal and regulatory point of view to the difficulties faced by those involved in clinical research, and to critically position the current hurdles against the backdrop of the existing legal and ethical framework. We investigated the EU guidance and the national approaches of all EU/EEA Member States, and critically discussed selected issues. We argue that the crisis may be an opportunity to foresee meaningful changes in the EU clinical trials framework post-COVID-19.