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Climate change and disease are two major threats to maintaining healthy seagrass habitats. Seagrasses, and the ecosystems they support, play a critical ecological role in global carbon (C) cycles, providing key ecosystem services, such as blue carbon storage. Zostera marina (eelgrass), the most widespread seagrass species globally, is increasingly affected by warming and is also regularly infected by the endophytic pathogen Labyrinthula zosterae. Both stressors negatively impact plant physiology and population distributions, yet the effects of these stressors on C cycling, and particularly on C metabolism and dissolved organic carbon (DOC) fluxes in eelgrass, remain largely unexplored. Through a mesocosm experiment simulating a marine heatwave (MHW) followed by pathogen challenge with L. zosterae, it was observed that the simulated MHW initially decreased daily community DOC fluxes and Net Production Rates (NPR), while not changing Respiration Rates. DOC released into the water column at the end of the MHW also was less bioavailable than DOC from the control treatment. Importantly, community NPR recovered to control levels after the simulated MHW was over, demonstrating the community's resilience to warming. On the other hand, plants challenged with L. zosterae, which caused a significant decrease in aboveground biomass, exhibited significant decreases in DOC and NPR up to 20 days after the infection. These results have important implications in blue carbon processes, given that both stressors significantly impact the quantity and quality of DOC produced by Z. marina communities. These findings also highlight the differing levels of resilience of C cycling in this system by showing that the impacts of the simulated heat wave may be more transient when compared to the effects of disease.