The influence of a wide range of CO2 levels on the growth, morphogenesis, and secondary metabolite production in vitro was evaluated. Shoots of thyme (Thymus vulgaris L.) and a spearmint–peppermint cross (Mentha spicata × Mentha piperita) were grown on MS medium with and without 3% sucrose under 350, 1500, 3000, 10,000, and 30,000 μL CO2/L for 8 weeks. Dichloromethane extracts from leafs were analyzed using GC-MS techniques. Prominent peaks were identified by comparison with known standards. Highest growth (i.e., fresh weight) and morphogenesis responses (i.e., leafs, shoots and roots) were obtained when shoots were grown under 10,000 μL CO2/L regardless of whether or not sucrose was included in the medium. Ultra-high CO2 concentrations (3000 μL CO2/L) stimulated secondary metabolite production regardless of whether or not the medium contained sucrose. However, the combination of certain ultra-high CO2 levels (e.g., 3000 to 10,000 μL CO2/L) and the presence of sucrose in the medium resulted in shoots producing the highest levels of secondary metabolites. These results suggest that in vitro photosynthesis, which is stimulated by ultrahigh CO2 levels, may enhance secondary metabolite production.