Phytoplankton play a pivotal role in regulating global ecosystem functions and biogeochemical cycles, responding to climate variability through changes in their biomass, diversity, community composition and physiology. Yet, the influence of climate change on their vertical distribution remains poorly understood, largely due to limited observations and the lack of explicit vertical parameterisation in most ocean ecosystem models. Here, we use CMIP6 climate projections to drive a two-layer ecosystem model, calibrated for two stratified ocean sites, to project future changes in phytoplankton vertical structure under different climate scenarios. Under high-CO2 emission pathways, we find a significant increase (decrease) in subsurface (surface) phytoplankton biomass at both sites. Conversely, under a sustainable CO2 emission pathway, the vertical structure remains relatively sta- ble. Our findings suggest that if we don’t reduce CO2 emissions, we may trigger a shift in the vertical distribution of phytoplankton, with unknown consequences for marine ecosystems and global biogeochemical cycles. Furthermore, relying solely on surface observations may obscure our understanding of how marine ecosystems respond to climate change.