The photorespiratory pathway, short photorespiration, is an essential process in oxygenic photosynthetic organisms but also reduces the efficiency of photosynthetic carbon assimilation and is hence frequently considered as a wasteful process. By comparing the response of wild-type plants and mutants impaired in photorespiration to a shift in ambient CO2 concentrations, we demonstrate that photorespiration also plays a beneficial role during short-term acclimation to reduced CO2 availability. Wild-type plants responded with few differentially expressed genes, mostly involved in drought stress, which is likely a consequence of enhanced opening of stomata and concomitant water loss upon shift toward low CO2. In contrast, mutants with impaired activity of photorespiratory enzymes were highly stressed and not able to adjust stomatal conductance to reduced external CO2 availability. The mutantsÂ´ transcriptional response was congruent, indicating a general reprogramming to deal with the consequences of reduced CO2 availability, signaled by enhanced oxygenation of ribulose-1,5 bisphosphate and amplified by the artificially impaired photorespiratory metabolism. Central in this reprogramming was the pronounced reallocation of resources from growth processes to stress responses. In conclusion, we demonstrate that unrestricted photorespiratory metabolism is a prerequisite for rapid physiological acclimation to a reduction in CO2 availability. Overall design: Leaf transcriptomes of Arabidopsis thaliana wild-type (WT) and photorespiratory mutants hpr1, shm1, glyk1, and pglp1, grown under high CO2 (HC; 1% CO2) conditions and shifted for 8 h to low CO2 (LC; 0.038% CO2) conditions. WT samples were sequenced in biological triplicates, all other samples in biological duplicates.