<jats:title>Abstract</jats:title><jats:p>Bottom trawling represents the most widespread anthropogenic physical disturbance to seafloor sediments on continental shelves. While trawling-induced changes to benthic ecology have been widely recognized, the impacts on long-term organic carbon storage in marine sediments remains uncertain. Here we combined datasets of sediment and bottom trawling for a heavily trawled region, the North Sea, to explore their potential mutual dependency. A pattern emerges when comparing the surface sediment organic carbon-to-mud ratio with the trawling intensity represented by the multi-year averaged swept area ratio. The organic carbon-to-mud ratio exhibits a systematic response to trawling where the swept area ratio is larger than 1 yr<jats:sup>−1</jats:sup>. Three-dimensional physical–biogeochemical simulation results suggest that the observed pattern is attributed to the correlated dynamics of mud and organic carbon during transport and redeposition in response to trawling. Both gain and loss of sedimentary organic carbon may occur in weakly trawled areas, whereas a net reduction of sedimentary organic carbon is found in intensely trawled grounds. Cessation of trawling allows restoration of sedimentary carbon stock and benthic biomass, but their recovery occurs at different timescales. Our results point out a need for management of intensely trawled grounds to enhance the CO<jats:sub>2</jats:sub> sequestration capacity in shelf seas.</jats:p>