Seagrass meadows form essential ecological components in coastal zones but are rapidly declining worldwide due to anthropogenic impacts, including eutrophication and climate change-related heat waves. An important consequence of increased eutrophication is organic matter input in the sediment, which, together with raised temperatures, stimulates the production of toxic sulfide. Although multiple recent studies have highlighted that seagrass can engage in a mutualistic relationship with lucinid bivalves alleviating sulfide toxicity in the rhizosphere, it remains unclear how this mutualism is affected by temperature and eutrophication. To unravel this relation, we investigated the response of the seagrass Zostera noltii to contrasting sediment organic matter conditions, temperatures and presence/absence of the lucinid clam Loripes orbiculatus in a full-factorial mesocosm experiment. Results demonstrate that temperature increased porewater sulfide and nutrient levels, particularly in treatments with high sediment organic matter content. Interestingly, L. orbiculatus reduced not only sulfide levels, but also porewater nutrients. The removal of sulfide in turn stimulated Z. noltii growth, despite lower nutrient availability. Finally, increased temperature suppressed the mutualistic benefit for Z. noltii as sulfide detoxification became hampered. We conclude that, as eutrophication remains an issue in the coastal zone and temperature extremes will likely become more common in the future, seagrass meadows where lucinids occur may need to increasingly rely on this mutualism. At the same time, however, this interaction will become more strained, with an inherent increasing risk of mutualism breakdown.