This dataset was built to feed a basin-wide spatial conservation planning exercise, targeting the deep sea of the North Atlantic, in the framework of the ATLAS H2020 project. This approach aimed to inform Marine Spatial Planning and conservation initiatives for the deep sea of the North Atlantic, by identifying conservation priority areas for the Vulnerable Marine Ecosystems (VMEs) and deep fish species and discussing the efficiency of the current spatial management context relatively to conservation stakes. This publication provides (1) the links to spatial datasets used as an input, (2) the R scripts used to run the final conservation scenarios together with associated table of targets and connectivity matrix, that can be run on the input data, and (3) the outputs of the final scenarios constructed and computed for ATLAS. Produced by IFREMER.