Elevated pCO2 may promote phytoplankton growth, and potentially alleviate carbon limitation during dense blooms. Under nitrogen-limited conditions, elevated pCO2 may furthermore alter the phytoplankton carbon: nitrogen (C:N) balance and thereby the synthesis of secondary metabolites, such as cyanobacterial toxins. A common group of these toxins are microcystins, with variants that not only differ in C:N stoichiometry, but also in toxicity. Here, we hypothesized that elevated pCO2 will increase the cellular C:N ratios of cyanobacteria, thereby promoting the more toxic microcystin variants with higher C:N ratios. To test this hypothesis, we performed chemostat experiments under nitrogen-limited conditions, exposing three Microcystis aeruginosa strains to two pCO2 treatments: 400 and 1200 μatm. Biomass, cellular C:N ratios and total microcystin contents at steady state remained largely unaltered in all three strains. Across strains and treatments, however, cellular microcystin content decreased with increasing cellular C:N ratios, suggesting a general stoichiometric regulation. Furthermore, as predicted, microcystin variants with higher C:N ratios generally increased with elevated pCO2, while the variant with a low C:N ratio decreased. Thus, elevated pCO2 under nitrogen-limited conditions may shift the cellular microcystin composition towards the more toxic variants. Such CO2 driven changes may have consequences for the toxicity of Microcystis blooms.