The ability to accurately measure organic carbon (OC) in marine sediments or soils is overall taken for granted in scientific communities, yet this seemingly mundane task remains a methodological challenge when the soil matrix contains calcium carbonate (CaCO3), creating inaccuracies in Blue Carbon estimates. Here, we compared five common methods combining acidification, combustion, and wet oxidation pre‐treatments for determination of OC in sediments and soils containing CaCO3 based on the analyses of artificial soil mixtures made of different OC and CaCO3 contents, and multiple soils from Australian seagrass cores. The results obtained showed that methods involving acidification pre‐treatment entailed −17 ± 0.2% (mean ± SE) underestimation of OC content (ranging from −8% to −26%), whereas the combustion‐based method was accurate for samples with high CaCO3 content but entailed 32–47% overestimation in samples with low CaCO3 content. The Heanes method (wet oxidation method) showed <5% deviation from the known OC content, but this method is not suitable for soil samples containing reduced iron, sulfur and potentially manganese compounds. The differences observed among methods have significant impacts on local, regional, and global Blue Carbon storage calculations. We provide key methodological guidelines for the analysis of OC in soils with high and low CaCO3 contents, aiming at improving accuracy in current Blue Carbon science.