Seagrass meadows are considered as global hotspots of blue carbon stocks. However, they suffer global cover loss mainly due to anthropogenic activities. Few is known on the impact of seagrass loss on their blue carbon stocks. This study investigates the impact of seagrass removal on soil organic carbon stocks two years after initial perturbation, and the potential bioturbation activity of co-existing burrowing shrimps in Gazi Bay, Kenya. Seagrass aboveground biomass was removed for a period of 18 months and organic carbon samples were taken 24 months after the first harvested at three depth layers (0-5cm, 5-10cm, 10-15cm). Results indicated that organic carbon was significantly lower in the 15cm depth profile sampled in harvested seagrass meadows. The sediment turnover rate of Callianassidae present in the bay was estimated at 948 ± 342 (SE) g.DW.d -1 . This bioturbation activity is assumed to play an important role in the potential release of sediment organic carbon stock from harvested plots. This study demonstrates the significant sub-surface organic carbon loss after seagrass removal, and the potential for burrowing shrimp to enhance organic carbon remineralisation. Further studies on tropical seagrass meadows organic carbon fate after seagrass loss to account for blue carbon budget.