The northern Scotia Sea contains the largest seasonal uptake of atmospheric carbon dioxide yet measured in the Southern Ocean. This study examines one of the main routes by which this carbon fluxes to the deep ocean, through the production of faecal pellets (FPs) by the zooplankton community. Deep sediment traps were deployed in two sites with contrasting ocean productivity regimes (P3, naturally iron-fertilized and P2, iron-limited), within the same water mass. The magnitude and seasonal pattern of particulate organic carbon (POC) and FPs in the traps was markedly different between the two sites. Maximum fluxes at P3 (22.91 mg C m−2 d−1; 2534 × 10 FP m−2 d−1) were an order of magnitude higher than at P2 (4.01 mg C m−2 d−1; 915 × 10 FP m−2 d−1), with flux at P3 exhibiting a double seasonal peak, compared to a single flatter peak at P2. The maximum contribution of FP carbon to the total amount of POC was twice as high at P3 (91%) compared to P2 (40%). The dominant FP category at P3 varied between round, ovoidal, cylindrical and tabular over the course of the year while, at P2, ovoidal FPs were consistently dominant, always making up more than 60% of the FP assemblage. There was also a difference in the FP state between the two sites, with FPs being relatively intact at P3, while FPs were often fragmented with broken peritrophic membranes at P2. The exception was ovoidal FPs, which were relatively intact at both sites. Our observations suggest that there was community shift from an herbivorous to an omnivorous diet from spring through to autumn at P3 while detritivores had a higher relative importance over the year at P2. Furthermore, the flux was mainly a product of the vertically migrating zooplankton community at P3 while the FP flux was more likely to be generated by deeper-dwelling zooplankton feeding on recycled material at P2. The results demonstrate that the feeding behavior and vertical distribution of the zooplankton community plays a critical role in controlling the magnitude of carbon export to the deep ocean in this region.