The aim of this research was to determine how changes in soil moisture and temperature influence ecosystem C fluxes in the context of changing grazing regimes in subalpine grasslands in the Pyrenees. We (i) measured CO2 fluxes in the field in cattle- and sheep- grazed areas, and (ii) compared responses of CO2 and CH4 fluxes from soil turf samples from cattle- and sheep-grazed areas to changes in soil temperature and moisture. The cattle-grazed area showed greater ecosystem respiration and gross ecosystem photosynthesis than the sheep-grazed areas. With respect to the temperature and moisture treatments, the two areas responded in a similar way: Soil moisture was the strongest driver of soil respiration rates; although temperature also increased CO2 effluxes from the soils, the effects were transient. The greatest effluxes of CO2 were found in soils incubated at elevated temperature and 80% soil moisture content. Methane fluxes were only influenced by the moisture treatment, with the greatest methane oxidation rates found at 40% soil moisture content. We conclude that regional changes in moisture availability resulting from climate change are likely to be the most important driver of soil respiration and methane fluxes in these grazed subalpine ecosystems.