Blue Carbon Ecosystems, including mangroves, salt marshes, and seagrass, are known for trapping organic matter and sequestering atmospheric carbon; however, they are also hotspots for land-based and sea-borne emerging contaminants. These contaminants, including microplastics and per- and poly-fluoroalkyl substances (PFASs), are increasingly degrading blue carbon ecosystems. Despite plastic and microplastics have gained substantial attention over the past decade, the combined effects of microplastics and co-contaminants (i.e., PFASs) on the unique biogeochemistry of blue carbon remain unclear. To investigate this, we conducted a controlled microcosm experiment to analyse the impact of microplastics, i.e. polyethylene terephthalate (PET) and polylactic acid (PLA), and PFAS (PFOA and PFOS) on blue carbon sediment biogeochemistry. Using high-resolution mass spectrometry (UHPLC-MS and FTICRMS) and microbial ecology techniques (16S amplicon sequencing), we examined the effects of microplastics and PFASs on biogeochemical processes. Our results showed that PFAS stimulated the microbial community to degrade organic matter and was responsible for a short-lived but intense greenhouse gas emission. The addition of PFAS supported methanogen growth, increasing methane emissions, while the PLA biopolymer supported fermentative sulphate-reducing bacteria, increasing CO2 emissions. Interactively, microplastics and PFAS affect biogeochemistry and greenhouse gas emissions more than does individually.