Individuating strategies to reduce greenhouse gas (GHG) emissions from agricultural soil, while preserving crop yield and the quality of products is needed. The major GHG emitted from agricultural soils is nitrous oxide (N2O) and its production is largely influenced by the amount of nitrogen (N) fertilizers applied and by the soil conditions, such as water content and temperature. The cultivation of processing tomato may lead to high N losses because it is characterized by a high frequency of irrigation events and N fertilizer applications. In this study we assessed the effect of reducing water from reintegration of 100% of water missing to field capacity (Ir2) to 50% (Ir1) and N applied, by 30% from 170 kg N ha-1 (N2) to 120 kg N ha-1 (N1) and 100% from N2 to 0 kg N ha-1 (N0), on yield, fruit quality and GHG emissions from soil in tomato cultivated under fertigation for two growing seasons (2014, 2015). We highlighted a great variability of results, both on GHG emissions from soil and on tomato productivity, due to differences in meteorological conditions in the two growing seasons. Higher marketable yield of tomato was recorded in N2 than in N1 only in 2014 and in Ir2 than Ir1 only in 2015, while reducing the agricultural inputs did not reduce the fruit quality. Carbon dioxide and nitrous oxide emissions were higher in 2015, while soil was a sink for methane in both growing seasons. We highlighted a general trend in lower nitrous oxide emissions with reduced water and N fertilizer rate, even if these emissions were largely variable in time and space. In particular, yield-scaled N2O emissions were lower in Ir1 than in Ir2, suggesting that a reduction of the irrigation level may be a suitable strategy for mitigating N2O emissions from tomato cultivated under fertigation in a Mediterranean environment.