Blue Carbon Ecosystems (i.e., mangrove, salt marsh, seagrass), widely known for trapping organic matter and pollutants, also trap a disproportionately large amount of plastics. Therefore, these ecosystems have become the hotspot of plastics and other co-contaminants either coming with plastics or separately through surface runoff. Although research on plastics has recently received increasing attention, the impacts of plastics along with their co-contaminants, especially in blue carbon ecosystems, are unknown. Therefore, through a controlled microcosm experiment, we have analysed the impacts of microplastics and nitrogen pollution on the biogeochemistry of blue carbon sediment. We employed high-resolution mass spectrometry and microbial ecology approaches in this study. Our study revealed that plastic, combined with nitrogen, emits more greenhouse gases than plastic or nitrogen separately. Similarly, plastic with nitrogen has synergistically impacted the microbial abundance, microbial functional mechanisms and metabolites, whereas only plastic has little impact on them.