The use of livestock waste as an organic fertiliser releases significant greenhouse gas emissions, exacerbating climate change. Innovative fertiliser management practices, such as treating slurry with plasma induction, have the potential to reduce losses of carbon and nitrogen to the environment. The existing research on the effectiveness of plasma-treated slurry at reducing nitrous oxide (N2O) and methane (CH4) emissions, however, is not comprehensive, although must be understood if this technology is to be utilised on a large scale. A randomised block experiment was conducted to measure soil fluxes of N2O and CH4 from winter wheat every two hours over an 83-day period using automated chambers. Three treatments receiving a similar amount of plant-available N were used: (1) inorganic fertiliser (IF); (2) pig slurry combined with inorganic fertiliser (PS); (3) plasma-treated pig slurry combined with inorganic fertiliser (TPS). Cumulative N2O fluxes from TPS (1.14 g N m−2) were greater than those from PS (0.32 g N m−2) and IF (0.13 g N m−2). A diurnal pattern in N2O fluxes was observed towards the end of the experiment for all treatments, and was driven by increases in water-filled pore space and photosynthetically active radiation and decreases in air temperature. Cumulative CH4 fluxes from PS (3.2 g C m−2) were considerably greater than those from IF (− 1.4 g C m−2) and TPS (− 1.4 g C m−2). The greenhouse gas intensity of TPS (0.2 g CO2-eq kg grain−1) was over twice that of PS (0.07 g CO2-eq kg grain−1) and around six times that of IF (0.03 g CO2-eq kg grain−1). Although treating pig slurry with plasma induction considerably reduced CH4 fluxes from soil, it increased N2O emissions, resulting in higher non-CO2 emissions from this treatment. Life-cycle analysis will be required to evaluate whether the upstream manufacturing and transport emissions associated with inorganic fertiliser usage are outweighed by the emissions observed following the application of treated pig slurry to soil.