Many studies have discussed the influence of elevated carbon dioxide (eCO2) on modeling and crop plants. However, much less effort has been dedicated to herbal plants. In this study, a robust monitoring for the levels of 94 primary and secondary metabolites and minerals in two medicinal herbs, basil (Ocimum basilicum L.) and peppermint (Mentha piperita L.), grwon under both ambient (aCO2, 360 ppm) and eCO2 (620 ppm) was performed. We also assessed how the changes in herbal tissue chemistry affected their biological activity. Elevated CO2 significantly increased herbal biomass, improved the rates of photosynthesis and dark respiration, and altered the tissue chemistry. Principal Component Analysis of the full data set revealed that eCO2 induced a global change in the metabolomes of the two plants. Moreover, Hierarchical Clustering Analyses showed quantitative differences in the metabolic profiles of the two plants and in their responsiveness to eCO2. Out of 94 metabolites, 38 and 31 significantly increased in basil and peppermint, respectively, as affected by eCO2. Regardless of the plant species, the levels of non-structural carbohydrates, fumarate, glutamine, glutathione, ascorbate, phylloquinone (vitamin K1), anthocyanins and a majority of flavonoids and minerals were significantly improved by eCO2. However, some metabolites tended to show species specificity. Interestingly, eCO2 caused enhancement in antioxidant, antiprotozoal, anti-bacterial and anticancer (against urinary bladder carcinoma; T24P) activities in both plants, which was consequent with improvement in the levels of antioxidant metabolites such as glutathione, ascorbate and flavonoids. Therefore, this study suggests that the metabolic changes triggered by eCO2 in the target herbal plants improved their biological activities.