The biological carbon pump is the mechanism by which the organic matter is exported or sequestered in the deep ocean from years to millennia. This downward transport is performed through physical transport of dissolved and particulate organic carbon, the sinking of particles or passive flux, and the active transport by diel and seasonal vertical migrants. The latter mechanism is still poorly studied, and seasonality of this active flux is even less known. We studied active flux by zooplankton in two transects from the productive coastal transition zone off Northwest Africa to the warm oligotrophic ocean. We estimated the metabolic activity from the surface to 900 m depth using the enzymatic activity of the electron transfer system (ETS) as a proxy for respiration. We found zooplankton ETS activity significantly higher during spring than during fall in the mesopelagic zone. Even at similar migrant biomass values, respiratory flux was higher during spring compared to fall due to the important differences in respiration rates in the mesopelagic zone. These striking differences of respiration rates in the mesopelagic zone was mainly due to the smaller body size of zooplankton during the productive season (spring). These results should be considered in models of active carbon export in the ocean. Here, we provide the data compiled during both cruises (spring and fall).