Acute climate events like marine heatwaves have the potential to temporarily or permanently alter community structure with effects on biodiversity and ecosystem services. We aimed to quantify the magnitude and consistency of climate driven community shifts inside and outside Marine Protected Areas before and after a marine heatwave using a kelp forest fish community dataset in southern California, USA. Abundance, biomass, diversity and recruitment of warm-water affinity species during the marine heatwave were significantly greater compared with prior years yet cool-water affinity species did not show commensurate declines. Fish communities inside MPAs were not buffered from these community shifts. This result is likely because the particular species most responsible for the community response to environmental drivers, were not fisheries targets. Resource managers working to preserve biodiversity in a changing climate will need to consider additional management tools and strategies in combination with protected areas to mitigate the effect of warming on marine communities.