Blue carbon ecosystems, including mangroves, saltmarshes, and seagrasses, mitigate climate change by storing atmospheric carbon. Previous blue carbon research has focused on organic carbon stocks. However, recent studies suggest that lateral inorganic carbon export might be equally important. Lateral export is a long-term carbon sink if carbon is exported as alkalinity (TAlk) produced via sulfate reduction coupled to pyrite formation. This study evaluates drivers of pyrite formation in blue carbon ecosystems, compares pyrite production to TAlk outwelling rates, and estimates global pyrite stocks in mangroves. We quantified pyrite stocks in mangroves, saltmarshes, and seagrasses along a latitudinal gradient on the Australian East Coast, including a mangrove dieback area, and in the Everglades (Florida, USA). Our results indicate that pyrite stocks were driven by a combination of biomass, tidal amplitude, sediment organic carbon, sediment accumulation rates, rainfall, latitude, temperature, and iron availability. Pyrite stocks were three-times higher in mangroves (103 ± 61 Mg/ha) than in saltmarshes (30 ± 30 Mg/ha) and seagrasses (32 ± 1 Mg/ha). Mangrove pyrite stocks were linearly correlated to TAlk export at sites where sulfate reduction was the dominant TAlk producing process. However, pyrite generation could not explain all TAlk outwelling. We present the first global model estimating pyrite stocks in mangroves, giving a first-order estimate of 197 Mg/ha (RMSE = 24 Mg/ha). In mangroves, estimated global TAlk production coupled to pyrite formation (∼3 mol/m2/y) is equal to ∼24% of their global carbon burial rate, highlighting the importance of including TAlk export in future blue carbon budgets.