Mangrove forests capture and store exceptionally large amounts of carbon and are increasingly recognised as an important ecosystem for carbon sequestration. Yet land-use change in the tropics threatens this ecosystem and its critical 'blue carbon' (carbon stored in marine and coastal habitats) stores. The expansion of shrimp aquaculture is among the major causes of mangrove loss globally. Here, we assess the impact of mangrove to shrimp pond conversion on ecosystem carbon stocks, and carbon losses and gains over time after ponds are abandoned. Our assessment is based on an intensive field inventory of carbon stocks at a coastal setting in Thailand. We show that although up to 70% of ecosystem carbon is lost when mangroves are converted to shrimp ponds, some abandoned ponds contain deep mangrove soils (>2.5 m) and large carbon reservoirs exceeding 865 t carbon per hectare. We also found a positive recovery trajectory for carbon stocks in the upper soil layer (0-15 cm) of a chronosequence of abandoned ponds, associated with natural mangrove regeneration. Our data suggest that mangrove carbon pools can rebuild in abandoned ponds over time in areas exposed to tidal flushing.