Reconstructions of past CO₂ concentrations rely on proxy estimates, with one line of proxies relying on the CO₂-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence ¹³C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.