Phototrophic protists are a fundamental component of the world's oceans by serving as the primary source of energy, oxygen, and organic nutrients for the entire ecosystem. Due to the high thermal seasonality of their habitat, temperate protists could harbour many well-adapted species that tolerate ocean warming. However, these species may not sustain ecosystem functions equally well. To address these uncertainties, we conducted a 30-day mesocosm experiment to investigate how moderate (12 °C) and substantial (18 °C) warming compared to ambient conditions (6 °C) affect the composition (18S rRNA metabarcoding) and ecosystem functions (biomass, gross oxygen productivity, nutritional quality – C:N and C:P ratio) of a North Sea spring bloom community. Our results revealed warming-driven shifts in dominant protist groups, with haptophytes thriving at 12 °C and diatoms at 18 °C. Species responses primarily depended on the species' thermal traits, with indirect temperature effects on grazing being less relevant and phosphorus acting as a critical modulator. The species Phaeocystis globosa showed highest biomass on low phosphate concentrations and relatively increased in some replicates of both warming treatments. In line with this, the C:P ratio varied more with the presence of P. globosa than with temperature. Examining further ecosystem responses under warming, our study revealed lowered gross oxygen productivity but increased biomass accumulation whereas the C:N ratio remained unaltered. Although North Sea species exhibited resilience to elevated temperatures, a diminished functional similarity and heightened compositional variability indicate potential ecosystem repercussions for higher trophic levels. In conclusion, our research stresses the multifaceted nature of temperature effects on protist communities, emphasising the need for a holistic understanding that encompasses trait-based responses, indirect effects, and functional dynamics in the face of exacerbating temperature changes.