Anthropogenic climate change is driven by increasing emissions of greenhouse gases (GHGs), and the three biogenic GHGs with the greatest effect on radiative forcing are carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). One mitigation strategy is to substitute fossil fuels with biomass-derived energy, so a thorough understanding of the GHG budget of energy crop production is needed. Agriculture’s biggest contribution to GHG emissions is N2O as a consequence of nitrogenous (N) fertiliser applications. Here two different novel automated systems, SkyBeam and SkyLine, are presented, capable of measuring net ecosystem exchange (NEE) of CO2, CH4 and N2O on a near-continuous basis. Unlike micrometeorological methods, SkyBeam and SkyLine resolve to the plot scale, enabling manipulative experimentation to further understanding GHG fluxes. In fully replicated experiments, the effects on GHG of compost addition and different N fertiliser types were investigated in Miscanthus x giganteus and oilseed rape (OSR, Brassica napus). A further comparison of soil GHG flux under a Miscanthus field and a conventional arable field was made using flux chambers. N2O made a major contribution to the GHG balance in the arable field (14% total soil flux) and from the OSR, where it reduced the GHG sink by ca. 50%. N2O flux was not a significant factor in Miscanthus, though compost addition increased N2O emission. Miscanthus was a net GHG source, attributed to CO2 emissions resulting from ploughing. Soil fluxes of N2O and CH4 were greater than those including vegetation. Strong diurnal patterns were seen in all three GHGs measured, and these differed between crops. N2O showed uptake during the day and emission at night from Miscanthus, whereas N2O emissions were largest during the day from OSR. Diurnal peaks in soil respiration occurred at 15.00 under barley (Hordeum vulgare) at and under Miscanthus at 20.00. Continuous measurements are vital to characterise the diurnal pattern of GHG flux, or can be used to direct appropriately-timed daily measurements to calculate GHG budgets.