Abstract Phytoplankton in the Southern Ocean strongly influence global biogeochemical cycles, but the region’s remoteness limits in situ monitoring. Satellite ocean color enables synoptic monitoring of phytoplankton dynamics by retrieving chlorophyll‐a concentration (Chl‐a). However, Southern Ocean optical properties deviate from global patterns, causing persistent ocean‐color anomalies and uncertain Chl‐a retrievals. These anomalies have been attributed to differences in either phytoplankton composition or non‐algal constituents relative to low‐latitude waters, but a unified explanation remains lacking. Using an extensive in situ data set, we show that phytoplankton size structure in Antarctic waters is fundamentally distinct from that in other ocean basins. Incorporating this distinct size distribution into an ocean‐color model, with the same underlying bio‐optical parameterizations, successfully reproduces the observed bio‐optical anomaly. Simulations further show that changes in size structure alter the bulk optical properties of both phytoplankton and non‐algal constituents. Tracking phytoplankton size structure is therefore essential for improving satellite Chl‐a trends and monitoring Southern Ocean biogeochemical cycles.