The stability of terrestrial carbon reservoirs is thought to be closely linked to variations in climate, but the magnitude of carbon–climate feedbacks has proved difficult to constrain for both modern and millennial timescales. Reconstructions of atmospheric CO2 concentrations for the past thousand years have shown fluctuations on multidecadal to centennial timescales, but the causes of these fluctuations are unclear. Here we report high-resolution carbon isotope measurements of CO2 trapped within the ice of the West Antarctic Ice Sheet Divide ice core for the past 1,000 years. We use a deconvolution approach to show that changes in terrestrial organic carbon stores best explain the observed multidecadal variations in the δ13C of CO2 and in CO2 concentrations from 755 to 1850 CE. If significant long-term carbon emissions came from pre-industrial anthropogenic land-use changes over this interval, the emissions must have been offset by a natural terrestrial sink for 13C-depleted carbon, such as peatlands. We find that on multidecadal timescales, carbon cycle changes seem to vary with reconstructed regional climate changes. We conclude that climate variability could be an important control of fluctuations in land carbon storage on these timescales.