To investigate the effect of nitrification inhibitors (NIs) 3,4-dimethylpyrazole phosphate (DMPP) and 3-methylpyrazole 1,2,4-triazole (3MP + TZ), on NO emissions and yield from a typical vegetable rotation in sub-tropical Australia we monitored soil NO fluxes continuously over an entire year using an automated greenhouse gas measurement system. The temporal variation of NO fluxes showed only low emissions over the vegetable cropping phases, but significantly higher emissions were observed post-harvest accounting for 50-70% of the annual emissions. NIs reduced NO emissions by 20-60% over the vegetable cropping phases; however, this mitigation was offset by elevated NO emissions from the NIs treatments over the post-harvest fallow period. Annual NO emissions from the conventional fertiliser, the DMPP treatment, and the 3MP + TZ treatment were 1.3, 1.1 and 1.6 (sem = 0.2) kg-N ha year, respectively. This study highlights that the use of NIs in vegetable systems can lead to elevated NO emissions by storing N in the soil profile that is available to soil microbes during the decomposition of the vegetable residues. Hence the use of NIs in vegetable systems has to be treated carefully and fertiliser rates need to be adjusted to avoid an oversupply of N during the post-harvest phase.