Seagrass meadows are natural carbon storage hotspots at risk from global change threats, and their loss can result in the remineralization of soil carbon stocks and CO2 emissions fueling climate change. Here we used expert elicitation and empirical evidence to assess the risk of CO2 emissions from seagrass soils caused by multiple human-induced, biological and climate change threats. Judgments from 41 experts were synthesized into a seagrass CO2 emission risk score based on vulnerability factors (i.e., spatial scale, frequency, magnitude, resistance and recovery) to seagrass soil organic carbon stocks. Experts perceived that climate change threats (e.g., gradual ocean warming and increased storminess) have the highest risk for CO2 emissions at global spatial scales, while direct threats (i.e., dredging and building of a marina or jetty) have the largest CO2 emission risks at local spatial scales. A review of existing peer-reviewed literature showed a scarcity of studies assessing CO2 emissions following seagrass disturbance, but the limited empirical evidence partly confirmed the opinion of experts. The literature review indicated that direct and long-term disturbances have the greatest negative impact on soil carbon stocks per unit area, highlighting that immediate management actions after disturbances to recover the seagrass canopy can significantly reduce soil CO2 emissions. We conclude that further empirical evidence assessing global change threats on the seagrass carbon sink capacity is required to aid broader uptake of seagrass into blue carbon policy frameworks. The preliminary findings from this study can be used to estimate the potential risk of CO2 emissions from seagrass habitats under threat and guide nature-based solutions for climate change mitigation.