Climate change is among the main threats to ecosystems, affecting biodiversity and ecosystem services. These changes are associated with increased atmospheric carbon dioxide concentration ([CO2]). This study aimed to investigate how [CO2] influences chlorophyll a fluorescence, vegetative growth, biomass production, and the number of root nodules (NRN) of Dimorphandra wilsonii, a critically endangered species. The study was conducted in six open‐top chambers with two CO2 levels, at elevated [CO2] (eCO2, 717 ± 77 ppm) and at ambient [CO2] (aCO2, 539 ± 42 ppm). We monitored vegetative growth weekly, and at the end of the experiment, we measured chlorophyll a fluorescence and biomass production. Dimorphandra wilsonii plants under eCO2 showed higher (p < 0.05) average leaf dry mass, average leaf area, and lower (p < 0.05) root/shoot ratio than plants under aCO2. The greater aerial biomass allocation contributes to maximizing the photosynthesis performance but could also result in the self‐shading of old basal leaves by new distal leaves on branches. This adjustment could be advantageous in the competition for light; however, it would be a disadvantage for below‐ground resource competition (such as water and nutrients), which could result in decreased drought resistance. Also, this adjustment would be unfavorable to D. wilsonii, which occurs in a seasonal climate environment competing with invasive grasses. Thus, it is possible that climate change scenarios with increases in [CO2] and drought periods could negatively influence the establishment of young plants of D. wilsonii in their natural occurrence area, which could worsen the conservation status of the species.