Livestock sheds are local and regional hotspots of greenhouse gases (GHG) emissions, but only very few studies analyse the intensities of GHG emissions from this source. The objective of this study was to quantify annual CH4, CO2 and N2O emissions from inside and outside of sheepfolds and summer cattle sheds in a typical agro-pastoral ecotone using static chamber technique. Both sheepfolds and cattle shed functioned as huge net sources of CH4 and N2O at annual scale. Animal presence increased CH4, CO2 and N2O effluxes for up to 1100 times compared to the animal sheds without animals. N2O emissions boosted for 160%–280% during and after rainfall and spring-thaw events. The CH4 and CO2 fluxes increased exponentially with faeces temperature for the outside sheepfold and summer cattle shed. The annual GHG emissions from both sheepfolds and summer cattle shed were 56 t CO2 equivalents ha−1, of which N2O contributed to 94%. Sheepfold dominated the total GHG emissions from animal sheds and accounted for 83% of the annual GHG flux. Annual emission on a per animal basis was 15, 0.2 and 28 kg CO2 eq year−1 sheep−1 and 26, 10 and 140 kg CO2 eq year−1 cattle−1 for N2O, CH4 and CO2, respectively. The annual N2O emissions from animal sheds were 70–250 times larger than nearby grassland soils, which were also net sink for atmospheric CH4. Concluding, animal sheds are very intensive local hotspots of GHG emissions, which should be considered at the local and regional scales. © 2021 British Society of Soil Science.