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Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO₂conditions. When light energy exceeds CO₂fixation capacity,Chlamydomonas reinhardtiiactivates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO₂Concentrating Mechanism (CCM). How light and CO₂signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO₂concentrations and that depletion of CO₂drives these responses, even in total darkness. High CO₂levels, derived from respiration or impaired photosynthetic fixation, repressLHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controllingLHCSR3andPSBStranscript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO₂and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO₂levels.