This dataset documents continuous physiological measurements of European beech (Fagus sylvatica) juveniles exposed to experimental low atmospheric CO₂ and subsequent recovery. Measurements were conducted in a controlled climate chamber experiment at the Karlsruhe Institute of Technology (KIT), Germany, between June 11 and June 28, 2025. The experiment consisted of two phases: a low CO₂ treatment phase (~58 ppm; June 11–22) designed to induce carbon starvation, followed by a recovery phase under ambient CO₂ conditions (June 22–28). Continuous measurements of branch and root CO₂ and H₂O fluxes were obtained at 40-minute intervals using an automated LI-COR gas exchange system. Concurrent stem diameter changes were recorded using electronic dendrometers to quantify short-term growth dynamics. Environmental variables, including soil and air temperature, were monitored throughout the experiment. Gas exchange data were baseline-corrected to account for chamber leakage and sensor drift. The dataset comprises 18,834 observations spanning all treatment phases and individuals. These data enable detailed analyses of whole-plant carbon fluxes, growth responses, and physiological recovery dynamics under experimentally induced carbon limitation. This integrated dataset enables investigation of carbon allocation trade-offs between immediate physiological responses, storage refilling, and growth during drought recovery from carbon starvation.