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 (PIC_eq). 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 did their pristine counterparts. However, the seagrass meadows’ mitigation services were largely constrained by both higher BC/TOC and PIC_eq/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 to ensure that greenhouse gas emitters do not exceed the ecosystems’ capacity.