Seagrass meadows store significant amounts of carbonate (CaCO3) in sediment, contributing to coastal protection but potentially offsetting their effectiveness as carbon sinks. Understanding the accumulation of CaCO3 and its balance with organic carbon (Corg) in seagrass ecosystems is crucial for developing seagrass-based blue carbon strategies for climate change mitigation. However, CaCO3 accumulation in seagrass meadows varies significantly across geographic regions, with notable data gaps in the Caribbean and Central America. Here, we sampled 10 seagrass meadows across an extensive island chain in The Bahamas, part of the largest seagrass ecosystem and one of the largest CaCO3 banks globally, to evaluate CaCO3 stock, accumulation rate, and its balance with Corg sequestration. Seagrass meadows in The Bahamas store 6405–8847 Tg of inorganic carbon (Cinorg) in the upper meter sediment, with an annual accumulation rate of 38.3–52.9 Tg of Cinorg, highlighting these meadows as hotspots for CaCO3 burial. CaCO3 contributes 67 ± 8%(mean ± standard error) of the sediment accumulation, indicating its important role in seabed elevation. Sediment Cinorg showed no significant relationship with Corg, with an average Corg : Cinorg ratio of 0.069 ± 0.002, ∼ 10 times lower than the threshold (Corg : Cinorg ratio of about 0.63) at which seagrass ecosystem transition from CO2 sources to sinks. However, the available air–sea gas flux measurement was only 1/5 of the calculated CO2 emission expected from calcification, suggesting that part of the accumulated CaCO3 is supported by allochthonous inputs. Furthermore, no perceivable relationship between seagrass density and either CaCO3 stock or accumulation rate was observed, indicating that seagrass may play a limited role in supporting CaCO3 production. Further studies on water chemistry, calcification rate, air–sea CO2 flux, and comparison between seagrass and unvegetated habitats are required to elucidate the carbon budget of this globally significant ecosystem.