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32 reviewsAlgal photosynthesis contributes to half of global carbon fixation and is enhanced by CO2-concentratingmechanisms (CCMs), which depend on the pyrenoid organelle in eukaryotic species. Despite its importance,the coordination between photosynthesis and other inorganic-carbon using pathways like fatty acid biosynthesis (FAS) remains underexplored. Here, we investigate this interplay using the green alga Chlamydomonasreinhardtii. We find that subunits of the acetyl-CoA carboxylase, key in FAS, form protein condensates at thepyrenoid periphery under limiting CO2 and redistribute throughout the chloroplast stroma under high CO2.The condensate structures form via liquid-liquid phase separation and are located in the pyrenoid’s outerlayer, which contains the bicarbonate-generating enzymes. Pyrenoid function-deficient mutants displayimpaired FAS, supporting a model where CCMs supply carbon to FAS. Our results unveil a moonlighting function of the pyrenoid and have implications for global carbon cycle, algal biotechnology, and the transfer ofpyrenoids into crops for photosynthesis improvements.