Blue carbon ecosystems (BCEs), which include seagrass meadows, tidal marshes and mangrove and supratidal forests, hold large reservoirs of organic carbon. Despite the impact of BCEs as natural climate solutions, the mechanisms responsible for carbon retention have not been clearly summarised, limiting our chance to manage BCEs for maximum carbon storage. Here, we explore a great mystery of the blue carbon cycle by reviewing existing published literature: Why is some coastal carbon remineralised into CO2 and CH4 by microbes within seconds/min while other carbon escapes microbial attack and becomes sequestered for millennia? The answer to this question will help predict and manage the global blue carbon cycle. We find that microbial communities are fundamental drivers of carbon mineralisation in BCE sediments, with their metabolic pathways dictating the fate of sequestered organic matter. Contrary to earlier notions, microbial diversity and composition are shown to significantly impact carbon stabilisation, with distinct microbial taxa targeting different organic compounds. Furthermore, anthropogenic disturbances such as habitat alteration and eutrophication can disrupt microbial communities, leading to increased carbon mineralisation and CO2 and CH4 emissions. Environmental parameters such as temperature, salinity, and nutrient availability also exert considerable influence on carbon stability in BCEs. Changes in these factors can alter microbial activity and the degradation rate of organic matter, highlighting the importance of understanding their additive and synergistic effects. For instance, warming combined with oxygen exposure due to habitat disturbance can amplify microbial carbon mineralisation, particularly in submerged BCEs like seagrass beds. Future research directions include characterising carbon at molecular levels, understanding region-specific drivers of carbon stability, and prioritising conservation efforts based on physiographic and geomorphologic settings. This review underscores the need for a holistic approach to BCE management, considering both microbial processes and environmental factors. By elucidating the factors governing carbon stability, this study aims to enhance our understanding of the role of BCEs in climate change mitigation and inform conservation strategies.