Anthropogenic pressures like ocean warming, acidification, rising N:P ratios, and marine heatwaves are affecting eukaryotic plankton diversity, though their combined impacts are rarely studied. To address this, we conducted a mesocosm experiment on a North Sea plankton community, testing the influence of a marine heatwave under ambient and future environmental conditions. Using 18S rRNA amplicon sequencing, we found that global change generally reduced protist diversity, in particular that of phototrophic organisms. While heterotrophs were largely unaffected by heatwaves, phototrophic diversity declined especially during cooling and only recovered under ambient conditions. Global change shifted the community from nano- to pico-sized phototrophs and increased harmful algae bloom species and parasites, while heatwaves elevated marine ochrophytes. The coccolithophore Gephyrocapsa oceanica thrived under both stressors. Our findings suggest that changing baseline conditions and extreme events can differentially impact heterotrophic and phototrophic diversity, with potential consequences for the metabolic balance of eukaryotic plankton communities.