Understanding how climate change will alter plankton dynamics in the Southern Ocean, a region of globally significant biogeochemical influence and strong seasonal variability, is critical for projecting the future of ocean ecosystems. Using a multi-model ensemble of 12 earth system models under the SSP5-8.5 climate-change scenario, we show that the seemingly stable Southern Ocean-wide plankton biomass masks opposing trends across three distinct biogeochemical zones. Plankton in the subpolar zone (40° S–60° S) remains near-stable owing to compensatory changes in bottom-up and top-down processes. In the subtropical zone (30° S–40° S) and seasonal ice zone (60° S–90° S), zooplankton decline and increase proportionally more than phytoplankton, constituting negative and positive trophic amplification, respectively. This trophic amplification is not uniformly distributed throughout the year but arises primarily from austral spring and summer. In the subtropical zone, shoaling-induced nutrient limitation reduces phytoplankton growth and concentration, causing a disproportionate decline in zooplankton grazing and biomass. In the seasonal ice zone, improved light availability from mixed-layer shoaling, sea-ice retreat, and warming enhance phytoplankton growth and surface concentration, driving disproportionately enhanced zooplankton grazing and biomass. In both zones, the seasonal trophic amplification signal is substantially stronger during the ecologically important spring and summer seasons than over the annual-mean, with potentially severe ecological consequences. Our results demonstrate that annual-mean projections could systematically underestimate both the magnitude and ecological severity of trophic amplification, and highlight the need for assessing seasonal and regional variations in plankton dynamics to better constrain future projections of Southern Ocean ecosystems.