Organic pollution is widespread in coastal areas and can have profound impacts on the seabed. Coastal sediments play an important role at a global scale in the recycling of organic matter, and this process is influenced by the habitat complexity of the sediments, among other factors. Mollusc shells are produced as a waste product from a range of anthropogenic activities, but we demonstrate that they can be used to increase the habitat complexity of sediments. We studied the effect of mussel-shell debris (shell-hash) on the biogeochemical processes of marine sediments affected by organic pollution, using a mesocosm experiment simulating the bioturbation effects of macrofauna. We found that shell-hash improved the ecological status of organically polluted sediments by reducing the accumulation of sulphide from anaerobic metabolic pathways. Additionally, when shell-hash was present in an organically polluted sediment, there was a decrease in ammonium release to the water column, thus preventing the negative ecological consequences of eutrophication. Synthesis and applications. Our study indicates that shell-hash debris can be used as a potential tool to mitigate the effects of organic enrichment on marine sediments. A density of shell-hash debris of 1900 g m−2 in the sediment can diminish toxic by-products (sulphides and ammonium) derived from the stimulation of anaerobic metabolic pathways by organic pollution, at levels that are biologically relevant. The mitigation effect of shell-hash is more pronounced in sediments where macrofauna is not present.