After years of great uncertainty on the viability of deep-sea mining activities, the International Seabed Authority is currently negotiating the draft regulations on exploitation of mineral resources in the Area. In this context, the EU has recently come up with a Commission proposal for an EU Council decision on the position to be taken on behalf of the EU at the meetings of the ISA organs. The proposal claims an exclusive EU competence for the negotiation of the draft, based on article 3 (2) of the Treaty on the Functioning of the European Union. In the light of the recent case law of the ECJ, this paper aims to discuss whether the EU does enjoy competence in the field of protection of the marine environment from the harmful effects of mining operations in the Area and, if so, its exclusive or shared nature. While the analysis will conclude that the EU is not attributed exclusive competence in this field, the paper will also consider the scenario by which the Council nonetheless obtains the necessary majority to negotiate the draft alone. In this respect, the conduct required from EU Member States in pursuance of the duty of sincere cooperation, and with a view to ensure coherence and consistency of the EU action in other international fora, is also explored.