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• Synthetic N fully replaced with composted manure reduced N-oxide emissions. • Bio-organic fertilizer application had the lowest yield-scaled N-oxide emission. • Soil N-oxide emissions were relevant during the fallow period. In order to reduce soil and environmental quality degradation associated with the use of synthetic nitrogen (N), substituting chemical fertilizer with organic or bio-organic fertilizer has become an increasingly popular option. However, components of this fertilizer strategy related to mitigation of soil N-oxide emissions and maintenance of crop yield remain uncertain. Here, we evaluated the effects of three different fertilizer strategies, with equal amounts of N, on nitrous oxide (N 2 O) and nitric oxide (NO) emissions, vegetable yield, and yield-scaled N 2 O and NO emissions under three consecutive cucumber growing seasons. The three treatments were chemical fertilizer (NPK, urea), organic fertilizer (O, composted cattle manure), and bio-organic fertilizer (O + T, O combined with Trichoderma.spp). Results showed that the NPK plot had the highest area-scaled emissions of N 2 O (13.1 ± 0.48 kg N ha−1 yr−1) and NO (5.01 ± 0.34 kg N ha−1 yr−1), which were 1.3–1.4 and 3.1–3.7 times greater than the O and O + T plots, respectively. The annual direct emission factors for N 2 O and NO were 2.08% and 0.92% for the NPK plot, which declined to 1.34% and 0.09% in the O plot, and 1.12% and 0.03% in the O + T plot, respectively. The annual vegetable yield was 117 ± 2.9 t ha−1 for NPK plot and 122 ± 2.0 t ha−1 for O + T plot, which was higher than 111 ± 1.7 t ha−1 for O plot. The yield-scaled N 2 O + NO emissions differed significantly with fertilization treatment, with the lowest value observed in the O + T plot. We attributed the lower soil N-oxide emissions following organic fertilizer application to the slow release of available N and enhanced denitrification caused by the increase of soil dissolved organic carbon and pH. Compared with the use of organic fertilizer alone, the addition of Trichoderma.spp significantly increased the potential denitrification rate but decreased N 2 O emissions, which may have promoted the reduction of N 2 O to N 2. Therefore, our results suggest that adopting composted organic fertilizer mixtures with microbial inoculants could be a win-win practice to mitigate gaseous N losses and simultaneously improve crop yield in intensively managed vegetable cropping systems. [ABSTRACT FROM AUTHOR]