In the last decades, the increasing necessity to reduce atmospheric carbon dioxide (CO2) concentrations has intensified interest in quantifying the capacity of coastal ecosystems to sequester carbon, referred to commonly as ‘Blue Carbon’ (BC). Among coastal habitats, seagrass meadows are considered as natural carbon sinks due to their capacity to store large amounts of carbon in their sediments over long periods of time. However, the spatial heterogeneity of carbon stocks in seagrass sediments needs to be better understood to improve the accuracy of BC assessments, particularly where there is high environmental variability. In the Mediterranean, Posidonia oceanica (L.) Delile constitutes extensive meadows considered as long-term carbon sinks due to the development of an exceptional structure known as ‘matte’, reaching several meters in height, which can be preserved over millennia. In order to specify the role of P. oceanica meadows in climate change mitigation, an estimate of carbon stocks has been conducted along the eastern coast of Corsica (NW Mediterranean). The approach is mainly based on the biogeochemical analysis of 39 sediment cores. Organic carbon (Corg; 327 ± 150 t ha−1, mean ± SE) and inorganic carbon stocks (Cinorg; 245 ± 45 t ha−1) show a high variability related to water depth, matrix (sandy vs rocky substrate) or the depositional environment (coastal vs estuary). The isotopic signature (δ13C) revealed a substantial contribution of allochthonous inputs of organic matter (macroalgae and sestonic sources) mainly in estuarine environment and shallow areas. The carbon stocks in the first 250 cm of matte (average thickness) were estimated at 5.6–14.0 million t Corg (study site) and 14.6–36.9 million t Corg (Corsica), corresponding to 11.6–29.2 and 30.4–76.8 years of CO2 emissions from the population of Corsica.