Greenhouse gas (GHG) fluxes from a seminatural, extensively sheep-grazed drained moorland and intensively sheep-grazed fertilised grassland in South East (SE) Scotland were compared over 4 yr (2007–2010). Nitrous oxide (N2O) and methane (CH4) fluxes were measured by static chambers, respiration from soil plus ground vegetation by a flow-through chamber, and the net ecosystem exchange (NEE) of carbon dioxide (CO2) by eddy-covariance. All GHG fluxes displayed high temporal and interannual variability. Temperature, radiation, water table height and precipitation could explain a significant percentage of seasonal and interannual variations. Greenhouse gas fluxes were dominated by the net ecosystem exchange of CO2 at both sites. Net ecosystem exchange of CO2 and respiration was much larger on the productive fertilised grassland (−1567 and 7157 g CO2eq m−2 yr−1, respectively) than on the seminatural moorland (−267 and 2554 g CO2eq m−2 yr−1, respectively). Large ruminant CH4 (147 g CO2eq m−2 yr−1) and soil N2O (384 g CO2eq m−2 yr−1) losses from the grazed grassland counteracted the CO2 uptake by 34%, whereas the small N2O (0.8 g CO2eq m−2 yr−1) and CH4 (7 g CO2eq m−2 yr−1) emissions from the moorland only impacted the NEE flux by 3%. The 4-yr average GHG budget for the grazed grassland was −1034 g CO2eq m−2 yr−1 and −260 g CO2eq m−2 yr−1 for the moorland.