The Southern Ocean has absorbed most of the excess heat associated with anthropogenic greenhouse gas emissions. Since Southern Ocean observations are sparse in certain regions and seasons, much of our knowledge of ocean heat uptake is based on climate model simulations. However, climate models still inadequately represent some properties of Southern Ocean clouds, and they have not identified the mechanisms by which clouds may affect Southern Ocean heat uptake (SOHU). Here, we use the ERA5 and JRA-55 reanalyses to assess the influence of clouds and other atmospheric processes on SOHU from 1979 to 2020. We find that years with the highest SOHU between 45° and 65°S are dominated by ocean heat uptake anomalies during winter and spring, but not during summer or fall. Winter and spring cloud cover are up to 7% higher when SOHU is up to 5.5 W/m² higher than the climatological seasonal mean, with the largest increases in the South Pacific Ocean. Clouds also contain more liquid water. These changes in cloud properties increase downwelling longwave radiation, amplifying ocean heat uptake. Cloud changes are also concomitant with a more stable lower atmosphere, which suppresses turbulent heat fluxes out of the surface. Overall, we find that SOHU is likely not mediated by enhanced surface shortwave absorption over the observational time period. A better understanding of how atmospheric processes impact ocean heat uptake may help improve our understanding of ocean heat uptake mechanisms in the current generation of climate models.