Colonies of mammals and sea birds are known hotspots for biogeochemical cycles with potentially large element stocks and fast turnover in the soil. Although penguin and seal colonies are sites with potentially extremely fast biogeochemical turnover, these sites as potential sources of GHG have largely been neglected. This study aims to quantify magnitudes and environmental drivers of GHG fluxes effected by the activity of Antarctic fur seal (Arctocephalus gazella) and King penguin (Aptenodytes patagonicus) in South Georgia, sub-Antarctica. In-situ CO ₂ and CH ₄ gas flux measurements were combined with laboratory incubations of intact soil cores collected from sites along two transects away from a seal and a penguin colony. Variations in laboratory incubations were consistent with the in-situ fluxes measured in February 2017, and showed high ecosystem respiration rates at colonies (mean 44.3 μg CO ₂ cm ⁻³ h ⁻¹ for seal colony, and 52.9–159 μg CO ₂ cm ⁻³ h ⁻¹ for penguin colony) and a marked decrease away from these hotspots. Moderate methane production rates were found within the colonies (mean 0.1 ng CH ₄ cm ⁻³ h ⁻¹ for seal colony, 44–145.5 ng CH ₄ cm ⁻³ h ⁻¹ for penguin colony), while relatively high consumption rates (mean −1.8 ng CH ₄ cm ⁻³ h ⁻¹ ) occurred outside the colonies. Incubations also included N ₂ O production rates, which were highly variable within the colonies (1.1–293 ng N ₂ O cm ⁻³ h ⁻¹ for seal colony, 0.8–594.7 ng N ₂ O cm ⁻³ h ⁻¹ for penguin colony) and decreased markedly to near zero away from the colonies. Bacterial and pmoA communities and drivers of GHG turnover and microbe community along both transects varied according to the sea animal activity intensity gradient. This is the first study at these latitudes to quantify the overall capacity of in-situ soil methane uptake at hot spots linked to sea animal colonies versus ambient conditions. All colony sites in this study were net sources of N ₂ O, while sites beyond colonies, which dominate the ice-free areas in South Georgia, were sinks of methane.