Mangroves in the Arabian Gulf provide several biological, ecological, and environmental services. They are also considered among the largest carbon sinks. However, mangroves along the coastlines of the Arabian Gulf have degraded in recent decades, mainly due to urbanization and coastal development. Therefore, restoration and afforestation programs have been initiated to enhance the services and functions of mangrove ecosystems and as part of national targets to mitigate climate change. Increasing carbon sinks by quadrupling the current areas covered by mangroves through afforestation programs by 2035 is one of the strategies to mitigate climate change in Bahrain. The aim of the present study was to estimate the organic carbon stocks in the sediments of natural and transplanted mangroves in Bahrain. Within the protected areas of Tubli and Arad Bays, sediment samples were taken down to a depth of 70 cm from natural and transplanted mangroves as well as a bare mudflat. The findings of the present study indicated that the total sediment organic carbon concentrations at three sampling sites of natural and transplanted mangroves and the mudflat were 200.54 ± 24.52, 112.36 ± 55.51, and 81.56 ± 8.92 Mg C/ha, respectively. The natural mangroves in Tubli Bay differed considerably from those in Arad Bay (p ≤ 0.001), based on the concentrations of organic carbon in sediments. However, there was a noticeable similarity seen in the organic carbon of the mangroves in Arad Bay that were transplanted 25 years prior and the natural mangroves in Tubli Bay, indicating the importance of a long-term mangrove afforestation strategy to mitigate climate change in the Arabian Gulf.