Estimates of global carbon stocks in coastal wetlands reveal that these are some of the most efficient carbon-sequestering environments in the world, which has prompted a renewed interest in conservation and restoration programs as an opportunity for greenhouse gas abatement. Accumulation of carbon in coastal wetlands is linked to diverse factors such as the type of vegetation, geomorphic setting, and sediment supply. Feedbacks between these factors and the tidal flow conditions drive the dynamics of carbon accumulation rates. Climate change-induced sea-level rise has been shown to increase the vulnerability to submergence of saltmarsh and mangroves in coastal wetlands, even if accommodation and landward colonization are possible. These potential losses of wetland vegetation combined with the reduced productivity of newly colonized areas will directly affect the capacity of the wetlands to sequester carbon from sediments and root growth. Here, we implement an eco-geomorphic model to simulate vegetation dynamics, soil carbon accumulation, and changes in soil carbon stock for a restored mangrove-saltmarsh wetland experiencing accelerated sea-level rise. We evaluate model outcomes for existing conditions and two different management scenarios aimed at mitigating sea-level rise effects and conserve wetland vegetation. Even though some management measures can result in partial conservation of wetland vegetation, they do not necessarily result in the best option for soil carbon capture. Our results suggest that accelerated sea-level can trigger accelerated wetland colonization resulting in wetland areas with limited opportunities for soil carbon capture from sediment and root mineralization, an issue that has not been considered in previous studies.