Bottom trawling is a non-selective commercial fishing technique whereby heavy nets and gear are pulled along the sea floor. The direct impact of this technique on fish populations and benthic communities has received much attention, but trawling can also modify the physical properties of seafloor sediments, water–sediment chemical exchanges and sediment fluxes. Most of the studies addressing the physical disturbances of trawl gear on the seabed have been undertaken in coastal and shelf environments, however, where the capacity of trawling to modify the seafloor morphology coexists with high-energy natural processes driving sediment erosion, transport and deposition. Here we show that on upper continental slopes, the reworking of the deep sea floor by trawling gradually modifies the shape of the submarine landscape over large spatial scales. We found that trawling-induced sediment displacement and removal from fishing grounds causes the morphology of the deep sea floor to become smoother over time, reducing its original complexity as shown by high-resolution seafloor relief maps. Our results suggest that in recent decades, following the industrialization of fishing fleets, bottom trawling has become an important driver of deep seascape evolution. Given the global dimension of this type of fishery, we anticipate that the morphology of the upper continental slope in many parts of the world’s oceans could be altered by intensive bottom trawling, producing comparable effects on the deep sea floor to those generated by agricultural ploughing on land.