The ubiquitous occurrence of microplastics in coastal habitats is widely reported. As an anthropogenic material with high carbon content, the contribution of microplastics to the coastal sediment carbon stock is still unassessed. Here, we report the occurrence pattern of microplastics (20-2000 μm) and estimate their contribution to the carbon stock in different coastal sediments in Hong Kong, a metropolis in the Pearl River estuary and part of the Greater Bay Area with a population of 70 million. Our data reveal that microplastics are more concentrated in the surface sediment and in vegetated coastal sediments. We also estimate that at present carbon from microplastics contributes between 0.001% and 1.197% to the sediment carbon pool at different depths. Despite the low contribution, microplastics have already made a hidden contribution to the coastal sediment carbon stock. Our data help to establish a baseline for future contributions of microplastics to total carbon storage in peri-urban coastal sediments.