Although zooplankton are the primary energy pathway from phytoplankton to fish, we understand little about how climate change will modify zooplankton communities and their role in marine ecosystems. Using a trait-based marine ecosystem model resolving key zooplankton groups, we assess climate change impacts on zooplankton community composition and implications for marine food webs globally. We find that future oceans favour food webs increasingly dominated by carnivorous (chaetognaths, jellyfish and carnivorous copepods) and gelatinous filter-feeding zooplankton (larvaceans and salps). By providing a direct energetic pathway from small phytoplankton to fish, the rise of gelatinous filter-feeders largely offsets the increase in trophic steps between primary producers and fish from declining phytoplankton production and increasing carnivorous zooplankton. However, our results indicate that future fish communities face not only reduced carrying capacity from falling primary production, but also lower quality diets as environmental conditions increasingly favour gelatinous zooplankton.