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Total organic carbon (TOC) sediment stocks as a CO2 mitigation service require exclusion of allochthonous black (BC) and particulate inorganic carbon corrected for water–atmospheric equilibrium (PICeq). For the first time, we address this bias for a temperate salt marsh and a coastal tropical seagrass in BC hotspots that represent two different blue carbon ecosystems of Malaysia and Australia. Seagrass TOC stocks were similar to the salt marshes with soil depths < 1 m (59.3 ± 11.3 and 74.9 ± 18.9 MgC ha-1, CI 95% respectively). Both ecosystems showed larger BC constraints than their pristine counterparts did. However, the seagrass meadows’ mitigation services were largely constrained by both higher BC/TOC and PICeq/TOC fractions (38.0% ± 6.6% and 43.4% ± 5.9%, CI 95%) and salt marshes around a third (22% ± 10.2% and 6.0% ± 3.1% CI 95%). The results provide useful data from underrepresented regions, and, reiterates the need to consider both BC and PIC for more reliable blue carbon mitigation assessments.