Frequent heat waves caused by climate change can give rise to physiological stress in many animals, particularly in sessile ectotherms such as bivalves. Most studies characterizing thermal stress in bivalves focus on evaluating the responses to a single stress event. This does not accurately reflect the reality faced by bivalves, which are often subject to intermittent heat waves. Here, we investigated the effect of intermittent heat stress on mitochondrial functions of the eastern oyster, Crassostrea virginica, which play a key role in setting the thermal tolerance of ectotherms. Specifically, we measured changes in mitochondrial oxygen consumption and H2O2 emission rates before, during and after intermittent 7.5°C heat shocks in oysters acclimated to 15 and 22.5°C. Our results showed that oxygen consumption was impaired following the first heat shock at both acclimation temperatures. After the second heat shock, results for oysters acclimated to 15°C indicated a return to normal. However, oysters acclimated to 22.5°C struggled more with the compounding effects of intermittent heat shocks as denoted by an increased contribution of FAD-linked substrates to mitochondrial respiration as well as high levels of H2O2 emission rates. However, both acclimated populations showed signs of potential recovery 10 days after the second heat shock, reflecting a surprising resilience to heat waves by C. virginica. Thus, this study highlights the important role of acclimation in the oyster's capacity to weather intermittent heat shock.