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Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO ₂ conditions. When light energy exceeds CO ₂ fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO ₂ Concentrating Mechanism (CCM). How light and CO ₂ signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO ₂ concentrations and that depletion of CO ₂ drives these responses, even in total darkness. High CO ₂ levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3 /CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO ₂ and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO ₂ levels.