AbstractSeagrass meadows are an important component of coastal ecosystems globally, and they capture and store organic carbon in living biomass and sediments. Geographical estimates of blue carbon in seagrass habitats are regionally biased, with limited information from the Indo-Pacific region, including Indonesia. Seagrass extent in Indonesia is declining rapidly, and it has been suggested that marine protected areas (MPAs) are an important instrument to support protection of seagrass ecosystems and their services. Thus, this study is aimed at quantifying and comparing sedimentary carbon stocks and sources of organic carbon from seagrass meadows located in undisturbed areas outside MPA, disturbed areas outside MPA, and within MPA in three small islands in Indonesia. The sediment carbon stocks from this study ranged from 19.81 to 117.49 Mg C ha−1, with the highest stock measured inside MPA (77.15 ± 1.38 Mg C ha−1), followed by undisturbed outside MPA (36.08 Mg C ha−1), and the lowest stock at disturbed outside MPA (21.86 ± 0.31 Mg C ha−1). The predominant source of organic carbon in disturbed meadows was from coastal POM (particulate organic matter, ~ 36%), while in MPA and undisturbed sites, the main source was from seagrass, with ~ 38% and ~ 60% contributions, respectively. The results of this study add more data and information on seagrass blue carbon potential from three different islands with different degrees of disturbance in Indonesia.