Abstract The European Union’s deep-sea fisheries regulations (Regulation (EU) No. 2016/2336) established obligations to manage deep-sea fisheries and to protect vulnerable marine ecosystems (VMEs). The European Commission is scheduled to complete a review of the regulations in 2021, providing an opportunity for new scientific information to be incorporated into the implementation of the regulations. Here, we summarise research outputs from the EU-funded Horizon 2020 ATLAS Project and explain their relevance to the regulation of deep-sea fisheries in EU waters. ATLAS research has increased our understanding of the distribution of VMEs and their importance in terms of ecosystem functioning. ATLAS research has also highlighted the utility of molecular techniques to understand fish population structure and the potential for habitat suitability models to help incorporate climate change into decision-making. Building on these scientific advances, we provide recommendations to help increase the effectiveness of management measures to conserve deep-sea fish stocks and protect VMEs.