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The fate of organic matter (OM) in the deep ocean remains enigmatic, with little understood regarding the flux and its utilization by deep food webs. We used compound-specific nitrogen stable isotope ratios of source amino acids measured in particle size classes and deep zooplankton (700–1500 m) to determine the contribution of small (0.7–53 μm) vs. large particles (> 53 μm) to their diet at four sites in the North Pacific. Our results show that small particles constitute between 9% and 98% of zooplankton diets, being the contribution higher at sites with lower flux regimes. The contribution of small particles to the diet of deep zooplankton was also higher when biomass of vertical migrators, and therefore actively transported OM, was lower. Climate-driven changes in primary production and export are expected to shift particle fluxes to smaller size classes, and thus their importance in midwater food webs may become more widespread.