The Southern Ocean’s role in the global methane (CH4) cycle remains uncertain due to limited measurement data from this remote region. It is unclear if the Southern Ocean acts as a source or sink of atmospheric CH4, and climatic changes can have consequences on the amount of marine CH4 released due to the acceleration of glacial melting and uncertain consequences on seabed CH4 reservoirs. Monitoring CH4 here is essential to understanding its impact on the global CH4 budget now and in the future. This study measured CH4 concentrations in both ocean and atmosphere during an expedition in the Scotia Sea, Weddell Sea, and South Georgia shelf, linking seabed activity, water column concentrations, sea-air fluxes, and atmospheric CH4 levels. All areas were found to be a small source of CH4 to the atmosphere. Surface water CH4 concentrations varied latitudinally, with lower CH4 levels south of the Southern Antarctic Circumpolar Current front, where upwelling brings CH4-depleted waters to the surface. On-shelf regions show higher CH4 emissions compared to off-shelf, with average sea-air CH4 fluxes of 0.269 ± 0.035 μmolm−2d−1 and 0.136 ± 0.021 μmolm−2d−1, respectively, likely due to seabed seepage and methane-enriched freshwater. This study finds that the Weddell and Scotia seas (including the South Georgia shelf) are a small source of atmospheric CH4. As this result contradicts previous studies identifying this region as a CH4 sink, continued monitoring is needed to understand how emissions are changing and may continue to change in the future.