Nitrogen (N) trace gas emission pulses produced after wetting dry soils may be important pathways of ecosystem N loss. However, the rates and mechanisms controlling these emissions remain unclear. We tested whether changes in microbial community structure and increased rates of atmospheric N deposition could explain N emissions at two desert sites differing in atmospheric N deposition by ~ six fold. We measured peak NOₓ (sum of nitric oxide and nitrogen dioxide) emissions 12 h post-wetting. NOₓ emissions remained elevated over 24 h and increased after adding N. In contrast, we measured the highest nitrous oxide (N₂O) emissions within only 15 min post-wetting. N₂O emissions decreased within 12 h, were insensitive to adding N, and were among the highest reported globally. Microbial communities at the high N deposition site were less diverse with higher 16S nitrifier and bacterial amoA gene abundances relative to the low N deposition site, suggesting an increased capacity for nitrification. Nevertheless, N emissions were lower at the high N deposition site. While microbial communities changed after wetting, these changes were not correlated with N emissions. We conclude that desert soils can produce substantial NOₓ and N₂O emission pulses, but that these emissions do not appear directly governed by changing microbial community characteristics or higher atmospheric N inputs. These findings highlight the importance of gaseous N loss pathways from dryland ecosystems that may contribute to sustained N limitation, with implications for atmospheric chemistry and Earth’s climate.