Elevated CO2 (eCO2) is one of the climate changes that may benefit plant growth under emerging soil contaminants such as heavy metals. In this regard, the morpho‐physiological mechanisms underlying the mitigating impact of eCO2 on beryllium (Be) phytotoxicity are poorly known. Hence, we investigated eCO2 and Be interactive effects on the growth and metabolism of two species from different groups: cereal (oat) and legume (alfalfa). Be stress significantly reduced the growth and photosynthetic attributes in both species, but alfalfa was more susceptible to Be toxicity. Be stress induced reactive oxygen species (ROS) accumulation by increasing photorespiration, subsequently resulting in increased lipid and protein oxidation. However, the growth inhibition and oxidative stress induced by Be stress were mitigated by eCO2. This could be explained, at least partially, by the increase in organic acids (e.g., citric acid) released into the soil, which subsequently reduced Be uptake. Additionally, eCO2 reduced cellular oxidative damage by reducing photorespiration, which was more significant in alfalfa plants. Furthermore, eCO2 improved the redox status and detoxification processes, including phytochelatins, total glutathione and metallothioneins levels, and glutathione‐S‐transferase activity in both species, but to a greater extend in alfalfa. In this context, eCO2 also stimulated anthocyanin biosynthesis by accumulating its precursors (phenylalanine, coumaric acid, cinnamic acid, and naringenin) and key biosynthetic enzymes (phenylalanine ammonia‐lyase, cinnamate hydroxylase, and coumarate:CoA ligase) mainly in alfalfa plants. Overall, this study explored the mechanistic approach by which eCO2 alleviates the harmful effects of Be. Alfalfa was more sensitive to Be stress than oats; however, the alleviating impact of eCO2 on Be stress was more pronounced in alfalfa.