The Southern Ocean plays a critical role in the uptake, transport and storage of carbon by the global oceans. It is the ocean’s largest sink of CO2, yet it is also among the regions with the lowest storage of anthropogenic carbon. This behaviour results from the unique combination of high winds driving the upwelling of deep waters and the subduction and northwards transport of surface carbon. Here we identify the indirect effect of climate-related changes in ocean conditions relative to the direct effect of anthropogenic changes in atmospheric CO2 on the reorganisation of carbon in the Southern Ocean using a combination of modelling and observations. We show that the effect of climate variability and climate change on the storage of carbon in the Southern Ocean is nearly as large as the effect of anthropogenic CO2 during the period 1998-2018 compared with a climatology around the year 1995. We identify a distinct climate fingerprint in dissolved inorganic carbon (DIC), with elevated DIC concentration in the surface ocean that reinforces the anthropogenic CO2 signal, and reduced DIC concentration in the subsurface ocean that offsets the anthropogenic CO2 signal. The fingerprint is strongest at lower latitudes (30°S-55°S). This fingerprint could serve to monitor the highly uncertain evolution of carbon within this critical ocean basin, and better identify its drivers.