The role of small prey (< 200 µm) in larval marine fish nutrition is largely understudied. Here, we explore the contribution of protozooplankton (PZP 20–200 µm) to larval fish diets, compared to metazoan microzooplankton (MZP 55–200 µm). More specifically, we tested whether the contribution of PZP increased during the low productivity season and decreased as larvae grow. We used North Sea autumn spawning herring (Clupea harengus) as a case study, as it is a key species with high commercial and ecological importance. In autumn and winter, the potential PZP and MZP prey wasdominated by cells < 50 µm (mainly Gymnodiniales,Pronoctiluca pelagica, Tripos spp. and Strombidium spp.), while copepod nauplii and copepodites where more abundant in autumn than in winter. Based on their trophic enrichment (∆15 N), larvae preferentially grazed on small MZP < 50 µm rather than PZP both in autumn and winter. Larvae of different body size (range 8–14 mm standard length) fed at the same trophic level but on different prey (similar δ¹⁵N but different δ¹³C). Growth rates (based on RNA/DNA estimates) were similar in autumn and winter, suggesting that growth was not affected by station-specific differences in the composition of the prey field. Our results not only underscore the important role of MZP on larval herring diets both in autumn and wintertime, but also emphasize the limitations of bulk stable isotope analysis. Given the current low recruitment in North Sea herring, these results provide significant information for future monitoring approaches relevant to stock assessment of this species.