Intensive vegetable fields, characterized by extremely high nitrogen (N) application rates, emit a large amount of the potent greenhouse gas nitrous oxide (N₂O). Short-term substitution of organic fertilizers for chemical fertilizers may mitigate N₂O emissions from vegetable fields. However, the long-term impacts, particularly on soil background N₂O emissions (excluding effects caused by newly applied fertilizers) in vegetable fields, remain poorly elucidated. Thus, we conducted an 11-year experiment to investigate the long-term fertilization effects on soil background N₂O emissions and the abundance of N-cycling genes in a greenhouse vegetable field. The soil capacity for potential denitrification activity (PDA) was further measured to evaluate denitrification potential. The field experiment comprised of four treatments: no fertilization (control, CK), only chemical N fertilizers (CF), 50 % of chemical N fertilizers substituted by organic fertilizers (OL), and 87.5 % of chemical fertilizers substituted by organic fertilizers (OH). The long-term application of chemical fertilizers alone (CF) and organic fertilizer substitutions (OL and OH) increased soil background N₂O emissions 30-fold and 10-fold, respectively, with average N₂O fluxes of 1.2 ± 3.8, 33.8 ± 5.1, 9.4 ± 2.3 and 10.2 ± 2.7 μg N₂O-N m⁻² h⁻¹ in the CK, CF, OL and OH treatment, respectively. The CF treatment significantly decreased the abundance of AOA amoA, nirS and nosZ genes, while both the OL and OH treatments increased the abundance of AOB amoA, and the OH treatment also increased nosZ gene abundance. Soil pH was a key determinant of the contrasting responses of N-cycling genes to different fertilizer types. Compared with low fertilizer substitutions (OL), high organic fertilizer substitutions (OH) did not result in more soil background N₂O emissions, despite higher potential denitrification activities and soil total N contents. This was due to increased abundance of nosZ gene and likely enhanced N₂O consumption activities. Soil NO₃⁻-N concentrations, soil pH, and the abundance of nosZ gene were three main factors in controlling the responses of soil background N₂O emissions to long-term fertilization. Overall, this study suggests that in the long-term perspective organic fertilizer substitution is a beneficial practice to mitigate N₂O emissions from intensive greenhouse vegetable cropping systems.