The importance of macrobenthos in benthic‐pelagic coupling and early diagenesis of organic carbon (OC) has long been recognized but has not been quantified at a regional scale. By using the southern North Sea as an exemplary area we present a modelling attempt to quantify the budget of total organic carbon (TOC) reworked by macrobenthos in seafloor surface sediments. Vertical profiles in sediments collected in the field indicate a significant but nonlinear correlation between TOC and macrobenthic biomass. A mechanistic model is used to resolve the bi‐directional interaction between TOC and macrobenthos. A novelty of this model is that bioturbation is resolved dynamically depending on variations in local food resource and macrobenthic biomass. The model is coupled to 3D hydrodynamic‐biogeochemical simulations to hindcast the mutual dependence between sedimentary TOC and macrobenthos from 1948 to 2015. Agreement with field data reveals a satisfactory model performance. Our simulations show that the preservation of TOC in the North Sea sediments is not only determined by pelagic conditions (hydrodynamic regime and primary production) but also by the vertical distribution of TOC, bioturbation intensity, and the vertical positioning of macrobenthos. Macrobenthos annually ingest 20%–35% and in addition vertically diffuse 11%–22% of the total budget of TOC in the upper‐most 30 cm sediments in the southern North Sea. This result indicates a central role of benthic animals in modulating the OC cycling at the sediment‐water interface of continental margins.