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Abstract Southern Ocean (SO) phytoplankton chlorophyll is highly variable on sub‐seasonal time scales. Although the SO is the windiest ocean basin globally, it is not conclusively understood how storms impact SO phytoplankton dynamics. Much of our existing knowledge stems from satellites, but biases due to data gaps from cloud cover and low solar angles remain unquantified. Here, we use ocean–sea‐ice simulations with the Community Earth System Model to quantify the climatological 1997–2018 imprint of storms on chlorophyll and phytoplankton dynamics in the ice‐free SO. Additionally, by comparing the full‐field model output to synthetic satellite observations, we quantify sampling biases in satellite‐derived estimates. We find that both the sign and the magnitude of the average surface chlorophyll imprint vary substantially across storms but last for at least 4 days after the storm passing. Based on our analysis, more than one third of the storms explain the majority of local non‐seasonal chlorophyll variability, but satellite‐derived storm imprints are often too large in magnitude. On the day of the storm passing, changes in vertical mixing predominantly cause surface chlorophyll anomalies, and reduced light availability due to enhanced cloud cover outweighs the enhanced nutrient availability due to entrainment. Interestingly, storms imprint differently on total net primary production than on surface chlorophyll, demonstrating the difficulty to derive carbon‐cycle impacts from a surface‐chlorophyll assessment. With SO future storm activity projected to increase, complementing satellite observations with other observing technologies, for example, profiling floats, is necessary to better constrain how storms impact biological carbon cycling in the SO.