The soil nitrogen (N) dynamics of an irrigated maize system in which stubble retention and stubble burned treatments were superimposed over treatments of varying N fertiliser rate were studied. The field site was near Whitton, New South Wales, Australia, and the work described here is part a life cycle analysis of greenhouse gas emissions from maize project. The objective of this part of the work was to quantify the fate of fertiliser N applied at the site. Field measurements of denitrification, mineral N content and recovery of ¹⁵N-labelled urea from microplots with and without ammonium thiosulfate were complimented with laboratory studies of denitrification and nitrous oxide (N₂O) flux. Significantly (P < 0.05) more fertiliser N was recovered in the grain from the stubble incorporated treatment than the stubble burned treatment and there was greater recovery of fertiliser N in the soil at the end of the experiment in the stubble burned treatment. This may indicate that fertiliser N applied to the stubble burned system may be more exposed to soil-N transformations. The reason for the difference in uptake and soil residual is not clear but may be related to soil structure differences leading to less plant accessibility of N in the burned treatment. This difference may lead to more nitrous oxide emission from soil in the stubble burned treatments. Short-term (1 h) static chamber measurements in the field found a strong N-rate dependence of N₂O emission rate for fertiliser rates between 0 and 300 kg N/ha. Inclusion of ammonium thiosulfate in the fertiliser formulation did not appear to have a significant impact on fertiliser N recovery.