Bottom trawling represents the most widespread anthropogenic physical disturbance to shelf sea sediments. While trawling-induced mortality in benthic fauna has been extensively investigated, its impacts on ecosystem functioning and carbon cycling at regional scales remain unclear. Using the North Sea as an example, we address these issues by synthesizing a high-resolution dataset of bottom trawling impact on sediments, feeding this dataset into a 3-dimensional physical–biogeochemical model to estimate trawling-induced changes in biomass, bioturbation and sedimentary organic carbon, and assessing model results with field samples. Results suggest a trawling-induced net reduction in macrobenthic biomass by 10-27%. Trawling-induced resuspension and reduction of bioturbation jointly and accumulatively reduce the regional sedimentary organic carbon sequestration capacity by 21-67%, equivalent to 0.58-1.84 Mt CO2 yr-1. Our study emphasizes the need for proper management of trawling on muddy seabeds, if the natural capacity of shelf seas for carbon sequestration should be conserved and restored.