Seagrass ecosystems are globally recognized to have significant carbon sequestration functions (‘blue carbon’), with an estimated carbon sequestration rate of 27.4 million tonnes yr^-1. Enhancing the stability of carbon storage is an important strategy for increasing carbon sequestration potential, thereby offering a natural solution for climate change mitigation. Biochar is widely used for promoting soil carbon storage stability in terrestrial ecosystems. The potential for similar functions of biochar in seagrass ecosystems is still unexplored. Here, we conducted a six-month field experiment to investigate the effects of biochar addition on tropical seagrass sediment ecology and biogeochemistry. We assessed the chemical (δ¹³C and sediment organic carbon (SOC) composition) and biological (extracellular enzyme activity and bacterial and fungal community structure and function) responses of biochar addition to seagrass sediment. We found that the biochar addition elevated the abundance of microbial r-strategists (e.g., Magnetospirillum, Azospirillum) and cellulose-decomposing Ruminiclostridium. This corresponded to higher dehydrogenase activity and an 8% reduction in labile sediment organic matter (LSOM). The 21% increase in refractory sediment organic matter (RefSOM) under biochar addition treatment was linked to inhibited lignin peroxidase activity, as well as fungal taxa (unclassified Didymellaceae and Mortierella). Further, the functional annotation analysis indicated that biochar addition promoted chemoheterotrophy and plant saprotrophy, aligning with the decomposition of LSOM and preservation of RefSOM. Our results provide novel evidence that biochar application can alter the sediment ecology in a way that enhances the stability of the seagrass SOC pools through interactions between microbial extracellular enzymes and sediment chemistry. This highlights biochar’s potential to strengthen the ‘blue carbon’ sink capacity in seagrass ecosystems.