Producing accurate structural maps is a pre-requisite to unravel the tectonic evolution of a region. For this purpose, magnetic anomaly maps are helpful data sets for the identification and mapping of geological features. We compiled 154 marine surveys and 7 aeromagnetic campaigns covering the Bay of Biscay, its surrounding continental shelves and western part of the Pyrenees. As the initial data sets had heterogeneous acquisition parameters, we applied a series of transforms before merging the data. We performed a variable reduction to the pole to localize the extrema of the anomaly vertically to their causative sources and facilitate geological interpretations. The resulting intermediate resolution maps compiled at 500 m altitude offshore and 3000 m both on- and offshore, display magnetic trends and patterns. They are enhanced by several potential field operators (analytic signal, tilt angle, vertical derivative) enabling the interpretation of the geometry of the sources causing the anomaly (3D, 2D and 2.5D). The analysis of these magnetic maps allows us to precise the distribution and segmentation of crustal domains previously identified in the Bay of Biscay and its adjacent continental shelves. A series of crustal scale structures mapped onshore and formed during and after the Variscan orogeny show well on this new map compilation, allowing the continuous onshore-offshore mapping of some of them and revealing their role in segmenting the northern margin of the Bay of Biscay. This new compilation notably reveals variations in the magnetic signature of the Ocean-Continent-Transition (OCT) that we interpret as related to an increased magmatic production of the eastern part of the Bay of Biscay OCT during continental breakup. In addition to precise previous structural maps, this new magnetic compilation opens new perspectives for the interpretation of the Bay of Biscay geodynamic setting.