Benthic communities play a major role in organic matter remineralisation and the mediation of many aspects of shelf sea biogeochemistry. Few studies have considered how changes in community structure associated with different levels of physical disturbance affect sediment macronutrients and carbon following the cessation of disturbance. Here, we investigate how faunal activity (sediment particle reworking and bioirrigation) in communities that have survived contrasting levels of bottom fishing affect sediment organic carbon content and macronutrient concentrations ([NH4-N], [NO2-N], [NO3-N], [PO4-P], [SiO4-Si]). We find that organic carbon content and [NO3-N] decline in cohesive sediment communities that have experienced an increased frequency of fishing, whilst [NH4-N], [NO2-N], [PO4-P] and [SiO4-Si] are not affected. [NH4-N] increases in non-cohesive sediments that have experienced a higher frequency of fishing. Further analyses reveal that the way communities are restructured by physical disturbance differs between sediment type and with fishing frequency , but that changes in community structure do little to affect bioturbation and associated levels of organic carbon and nutrient concentrations. Our results suggest that in the presence of physical disturbance, irrespective of sediment type, the mediation of macronutrient and carbon cycling increasingly reflects the decoupling of organism-sediment relations. Indeed, it is the traits of species that reside at the sediment-water interface, or that occupy deeper parts of the sediment profile, that are disproportionately expressed post-disturbance, not necessarily the traits that are most important for sustaining biogeochemical functioning.