Globally, sub-optimal use of nitrogen (N) fertiliser and elevated N irrigation groundwater have led to high leached nitrate (NO3−) losses from protected vegetable field systems. Optimising fertiliser and irrigation management in different soil types is crucial to reduce future N loads from such systems. The present 4-year study examined leached N loads from lysimeter monitoring arrays set up across 18 protected vegetable system sites encompassing the dominant soil types of northern China. The treatments applied at each field site were: 1) a high N and high irrigation input treatment (HNHI); 2) a low N but high irrigation input treatment (LNHI) and 3) a low N with low irrigation input treatment (LNLI). Results showed that the mean annual leached total nitrogen loads from the HNHI, LNHI and LNLI treatments were 325, 294 and 257 kg N ha−1 in the fluvo-aquic soil, 114, 100 and 78 kg N ha−1 in the cinnamon soil and 79, 68 and 57 kg N ha−1 in the black soil, respectively. The N dissolved in irrigation water in the fluvo-aquic soil areas was 8.26-fold higher than in the cinnamon areas. A structural equation model showed that N fertiliser inputs and leaching water amounts explained 14.7 and 81.8% of the variation of leached N loads, respectively. Correspondingly, reducing irrigation water by 21.5% decreased leached N loads by 20.9%, while reducing manure N and chemical N inputs by 22 and 25% decreased leached N loads by only 9.5%. This study highlights that protected vegetable fields dominated by fluvo-aquic soil need management to curtail leached N losses in northern China.