For over 50 years, the conceptualisation of low-nutrient oligotrophic systems having longer food chains and thus lower energy transfer to fish than their high-nutrient eutrophic counterparts1 has achieved the status of an ecological paradigm. However, recent global assessments indicate global fish biomass could be much higher than previously thought2–4, suggesting that our traditional understanding of food webs may need to be revisited. Here, we challenge the classical paradigm by exploring the role of zooplankton in food webs across the world’s oceans. Using observed zooplankton size spectra, and output from a size-spectrum model that resolves nine zooplankton groups, we conclude that food chains in oligotrophic (low-nutrient) and eutrophic (high-nutrient) systems have similar lengths. We offer a compelling hypothesis to explain this emergent pattern: self-organisation of zooplankton groups across the global productivity gradient regulates food chain length. We find that in oligotrophic systems the increased carnivory and longer food chains are offset by relatively large gelatinous filter feeders eating the dominant small phytoplankton, resulting in shorter-than-expected food chains, but decreasing food quality for fish. Our findings highlight the pivotal role zooplankton play in regulating energy transfer. Better resolution of zooplankton groups, their feeding relationships and carbon content in models will increase our ability to estimate current global fish biomass 5, project future fish biomass under climate change6–8, and provide more-robust forecasts of nutrient9 and carbon cycling10.