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Summary: Primary production in the Southern Ocean is dominated by diatom‐rich phytoplankton assemblages, whose individual physiological characteristics and community composition are strongly shaped by the environment, yet knowledge on how diatoms allocate cellular energy in response to ocean acidification (OA) is limited. Understanding such changes in allocation is integral to determining the nutritional quality of diatoms and the subsequent impacts on the trophic transfer of energy and nutrients.Using synchrotron‐based Fourier transform infrared microspectroscopy, we analysed the macromolecular content of selected individual diatom taxa from a natural Antarctic phytoplankton community exposed to a gradient of fCO2 levels (288–1263 µatm).Strong species‐specific differences in macromolecular partitioning were observed under OA. Large taxa showed preferential energy allocation towards proteins, while smaller taxa increased both lipid and protein stores at high fCO2.If these changes are representative of future Antarctic diatom physiology, we may expect a shift away from lipid‐rich large diatoms towards a community dominated by smaller taxa, but with higher lipid and protein stores than their present‐day contemporaries, a response that could have cascading effects on food web dynamics in the Antarctic marine ecosystem. [ABSTRACT FROM AUTHOR]