Anthropogenic stressors from climate change can affect individual species, community structure, and ecosystem function. Marine heatwaves (MHWs) are intense thermal anomalies where water temperature is significantly elevated for five or more days. Climate projections suggest an increase in the frequency and severity of MHWs in the coming decades. While there is evidence that marine protected areas (MPAs) may be able to buffer individual species from climate impacts, there is not sufficient evidence to support the idea that MPAs can mitigate large-scale changes in marine communities in response to MHWs. California experienced an intense MHW and subsequent El Niño Southern Oscillation event from 2014 to 2016. We sought to examine changes in rocky reef fish communities at four MPAs and associated reference sites in relation to the MHW. We observed a decline in taxonomic diversity and a profound shift in trophic diversity inside and outside MPAs following the MHW. However, MPAs seemed to dampen the loss of trophic diversity and in the four years following the MHW, taxonomic diversity recovered 75% faster in the MPAs compared to reference sites. Our results suggest that MPAs may contribute to long-term resilience of nearshore fish communities through both resistance to change and recovery from warming events.