Despite the relatively small proportion of ocean surface they represent, continental shelf ecosystems are among the most productive in the world. Located at the interface between terrestrial and marine environments, these habitats are structured by strong environmental forcings, especially on the sea bottom. A clear understanding of the spatial distribution of these habitats, along with knowledge on the composition and functioning of their associated communities, is essential for fisheries management and ecosystem conservation. Here, we used data from yearly EVHOE otter trawl surveys (2008–2020) to characterize the spatial structuration of benthic communities of the entire continental shelf of the Bay of Biscay (France), and to investigate the potential environmental drivers of these patterns. Two separate biological components were studied: epibenthic megainvertebrates and bentho-demersal fish. Clustering analyses identified seven assemblages within each component. We detected a strong correlation between the spatial organization of the different assemblages identified for fish and megainvertebrates, providing evidence for broad-scale spatial structuration of benthic habitats—benthiscapes—in this shelf ecosystem. The most influential environmental variables were identified as bottom temperature, sediment type, and primary production. Patterns in certain structural parameters, such as biomass, revealed possible spatial differences in ecological functioning. For example, we observed a drop in biomass from the coast to the central part of the shelf, followed by an increase in biomass near the edge of the Armorican shelf. These patterns reflect major large-scale processes (river inputs versus shelf-break upwelling) structuring the entire Bay of Biscay ecosystem. A comparative analysis revealed that the biological features and functioning observed in this study are shared with other European continental shelves. In addition to improving our knowledge of benthic environments, studies such as this one can promote improvements in ecosystem-based management and marine spatial planning of a fast-changing ecosystem under multiple anthropogenic stresses.