Mangrove ecosystems are threatened by a variety of anthropogenic changes, including climate change. The main aim of this research is to quantify the spatial variation in the different mangrove carbon stocks, aboveground carbon (AGC), belowground carbon (BGC), and soil carbon (SOC), under future climate scenarios. Additionally, we sought to identify the magnitude of sea-level rise (SLR) exposure with the view of identifying the mangrove regions most likely to face elevated inundation. Different representative concentration pathways (RCPs) ranging from the most optimistic (RCP 2.6) to medium emissions (RCP 4.5) and the most pessimistic (RCP 8.5) were considered for 2070. We used the Marine Ecoregions of the World (MEOW), a biogeographical classification of coastal ecosystems, to quantify the variation in future carbon stocks at a regional scale and identify areas of potential carbon stock losses and gains. Here, we showed that the mangroves of Central and Western Indo-Pacific islands (Andamans, Papua New Guinea, and Vanuatu), the west African coast, and northeastern South America will be the worst hit and are projected to affect all three carbon stocks under all future scenarios. For instance, the Andaman ecoregion is projected to have an 11–25% decline in SOC accumulation, while the Western Indo-Pacific realm is projected to undergo the sharpest declines, ranging from 10% to 12% under all three scenarios. Examples of these areas are those in Amazonia and the eastern part of South Asia (such as in the Northern Bay of Bengal ecoregion). Based on these findings, conservation management of mangroves can be conducted.