Marine phytoplankton community composition influences the production and export of biomass and inorganic minerals (such as calcite), contributing to core marine ecosystem processes that drive biogeochemical cycles and support marine life. Here we use morphological and assemblage data sets within a size‐trait model to investigate the mix of cellular biogeochemical traits (size, biomass, calcite) present in high latitude calcareous nannoplankton communities through the Oligocene (ca. 34–26 Ma) to better understand the biogeochemical consequences of past climate variability on this major calcifying phytoplankton group. Our record from IODP Site U1553 in the southwest Pacific reveals that nannoplankton communities were most size diverse during the earliest Oligocene, which we propose is linked to evidence for increased nutrient availability in the region across the Eocene‐Oligocene transition. In addition to driving changes in community size structure, early Oligocene extinctions of the largest Reticulofenestra species combined with an increasing dominance of heavily calcified, small‐medium‐sized cells through time also led to an overall increase in community inorganic to organic carbon ratios (PIC:POC) throughout the Oligocene. Crucially, genus‐level cellular PIC:POC diversity meant that abundance was not always the best indicator of which species were the major contributors to community biomass and calcite. As shifts in plankton size structure and calcareous nannoplankton PIC:POC have previously been highlighted as important in biological carbon pump dynamics, our results suggest that changes in community composition that are coupled to changes in community biogeochemical trait diversity have the potential to significantly alter the role of calcareous nannoplankton in marine biogeochemical processes.