Deep-sea ecosystem processes play a key role in global functioning of the planet. These functions are largely dependent upon deep-sea biodiversity. Industrial fisheries, after the depletion of fish stocks and destruction of the marine habitats on continental shelves, are now rapidly moving deeper into the ocean interior. We show here that bottom trawling along continental slopes has a major impact on deep-sea sedimentary ecosystems, causing their degradation and infaunal depauperation. Deep-sea fisheries, indeed, cause the collapse of benthic biodiversity and ecosystem functions, with potential consequences on the biogeochemical cycles. These findings support the claim of immediate actions for a sustainable management of fisheries in deep-sea environments.