Abstract Marine heatwaves are increasing globally in intensity and duration. To investigate the potential consequences for coastal ecosystems, the effects of short‐term heat stress must be better understood. This study examined eco‐physiological responses in two common intertidal bivalves, Cerastoderma edule and Macoma balthica , to different heatwave intensities in a mesocosm experiment under near‐natural environmental conditions. Single‐species assemblages were exposed to a 15‐d heatwave of either +2.8°C (mild heatwave) or +4.4°C (strong heatwave) above ambient temperatures. Survival and condition were monitored, and filtration rates were measured before and during heatwave exposure to investigate feeding behavior. Bivalve respiration rates were measured before, during, and after heatwave exposure as a proxy for metabolic responses. For C. edule , we found significantly elevated filtration rates during the mild but not the strong heatwave. For M. balthica , survival was similar across treatments, but marine heatwaves had a significant effect on the condition index (tissue/shell mass ratio). During heatwave exposure, respiration rates were similar across treatments for both species. However, following the heatwaves, bivalves previously exposed to a strong heatwave showed lower respiration rates compared to those exposed to an ambient or a mild heatwave. This study revealed that short‐term heatwaves can have persisting negative effects on bivalve metabolism and that the two species responded differently to the heatwave intensities. Further research is needed on the potential long‐term effects of marine heatwaves on intertidal fauna and their capacity to continue providing crucial ecosystem services.