Marine heatwaves (MHWs) are episodes of anomalous warming in the ocean that can last from a few days to years. MHWs have different characteristics in terms of intensity, duration and frequency and generate thermal stress in marine eco- systems. In reef ecosystems, they are one of the main causes of the decreased presence and abundance of corals, invertebrates and fish. The deleterious capac- ity of thermal stress often depends on biotic factors, such as the trophic control of predators on prey. Despite the evidence of thermal stress and biotic factors affecting individual species, the combined effects of both stressors on entire reef ecosystems are much less studied. 2. Here, using a food web modelling approach, we estimated the rate of change in species' biomass due to different MHW characteristics. Specifically, we modelled the mechanistic link between species' consumption rate and seawater tempera- ture (thermal stressor), simulating species' biomass dynamics for different MHW characteristics under different trophic control assumptions (top-down, mixed trophic control and bottom-up). 3. We find that total reef ecosystem biomass declined by 10% ± 5% under MHWs with severe intensity and a top-down control assumption. The bottom-up con- trol assumption moderates the total ecosystem biomass reduction by 5% ± 5%. Irrespective of the MHW characteristics and the trophic control assumption, the most substantial biomass changes occur among top, mesopredators and corals (5% to 20% ± 10%). 4. We show that reef ecosystems where predators exert top-down control on prey are prone to suffer species abundance declines under strong MHW events. We identify food web trophic control as a crucial driver that modulates the impacts of MHWs. Overall, our results provide a unified understanding of the interplay be- tween abiotic stressors and biotic factors in reef ecosystems under extreme ther- mal events, offering insights into present baselines and future ecological states for reef ecosystems.