Conservation of ecosystems is an important tool for climate change mitigation. Seagrasses, mangroves, saltmarshes and other marine ecosystems have particularly high capacities to sequester and store organic carbon (blue carbon), and are being impacted by human activities. Calls have been made to mainstream blue carbon into policies, including carbon markets. Building on the scientific literature and the French voluntary carbon standard, the ‘Label Bas-Carbone’, we develop the first method for the conservation of Posidonia oceanica seagrasses using carbon finance. This methodology assesses the emission reduction potential of projects that reduce physical impacts from boating and anchoring. We show how this methodology was institutionalized thanks to a tiered approach on key parameters including carbon stocks, degradation rates, and decomposition rates. We discuss future needs regarding (i) how to strengthen the robustness of the method, and (ii) the expansion of the method to restoration of seagrasses and to other blue carbon ecosystems.