Climate change is predicted to increase the frequency, severity, and duration of extreme climatic events such as heatwaves. Benthic organisms inhabiting intertidal flats are subjected to both marine and atmospheric heatwaves and can experience extreme temperature variations over relatively short periods of time. Non-indigenous species are generally capable to cope with extreme events more efficiently that native species. The Arcachon bay, a lagoon located along the French Atlantic coast is currently colonised by the invasive mussel, Arcuatula senhousia. In this study, we investigated how these two stressors (non-indigenous species colonisation and heatwaves) affect soft-bottom ecosystem functioning. We conducted two seasonal laboratory experiments to investigate the effects of combined marine and atmospheric heatwaves on the biogeochemical dynamics of sediments colonised by A. senhousia at different densities. More precisely, we assessed the community scale responses by measuring nutrients (NOx, NH4+, PO43-) and oxygen fluxes across the sediment-water interface. The results highlight that (1) heatwaves affect oxygen and nutrient exchanges across the sediment-water interface, (2) the magnitude of these effects can be strongly enhanced by increasing densities of A. senhousia, and (3) a marked seasonal-dependence. These results emphasise that the interaction between the seasonality of heatwave occurrence, its intensity and the level of colonisation by non-indigenous ecosystem engineers likely shape their consequences for ecosystem functioning. Our results thus reinforce previous findings suggesting that climate change may profoundly exacerbate the effects of biological invasions.