Micronekton plays a significant but often overlooked role in carbon transport within the ocean. Using a one-dimensional trait-based model, we simulated the diel vertical migrations of micronekton and their carbon production through respiration, fecal pellets, excretion, and dead bodies. Our model allowed us to explore the biotic and abiotic variables influencing the active transport of carbon in the mesopelagic zone. The functional approach highlighted the importance of size and taxonomy, in particularly considering fish, crustaceans, and cephalopods as key factors controlling the efficiency of carbon transport. Several metabolic parameters accounted for most of the variability in micronekton biomass, organic carbon production, and transport efficiency, mostly linked to respiration rates. Our results suggest that in temperate regions, the export of particles in the mesopelagic zone induced by micronekton is greater in summer, with active carbon transport reaching 18 mgC m−3 y−1. However, in the context of global warming, the evolution of the impact of micronekton on carbon sequestration remains uncertain. This underscores the imperative for future research to deepen our understanding of micronekton metabolism and vertical dynamics through a functional approach and in relation to their environment.