AbstractBenthic metabolism and net carbon accumulation in mangroves sediments strongly depend on the quantity and quality of organic matter (OM) supplied, including material brought by coastal waters such as the macroalgae Sargassum spp. Mesocosms were used to assess the effect of eutrophication by Sargassum on mangrove sediments. The concentration of fatty acids (FAs), organic carbon and its carbon isotopic signature, and the sediments–air CO2 fluxes were used to follow the evolution of sedimentary OM in surface and subsurface sediments for 60 d. Sargassum beaching shifted microbial and crab metabolism, leading to a preferential degradation of the labile fraction of OM from both Sargassum (δ13C = −17.7‰ and high concentration of essential FAs) and mangrove leaves (δ13C: −28.9‰ and high concentrations of 18:2ω6 and 18:3ω3). Fatty acids composition of crabs hepatopancreas revealed they preferentially fed on Sargassum and these invertebrates also increased the particulate OM tidal export. In addition, microbial activity at the sediment surface was enhanced, as revealed by strong production of branched FAs and higher CO2 fluxes in mesocosms containing Sargassum. However, Sargassum beaching also increased the transfer and preservation of more refractory OM from mangrove leaves found in higher quantity in subsurface sediments (6–8 cm) after 60 d. Inputs of macroalgae induced a negative priming effect and enhanced the preservation of blue carbon in the sediments. This negative priming effect was enhanced by crab activities. These biotic interactions that include microbial communities apparently make mangrove efficient in storing carbon in a context of growing eutrophication of the tropical ocean.