•No-tillage significantly increased soil CO2 emissions at the highest N-fertilizer rate.•Soil CO2 emission depends on soil temperature and moisture.•Soil acted as a CH4 sink in all treatments.•Reduced and no-tillage increased above-ground C-inputs at the highest N-fertilizer rate. In newly irrigated Mediterranean agroecosystems, the combined effect of tillage and N fertilization on soil carbon dioxide (CO2) and methane (CH4) fluxes is at present poorly understood. The goal of this study was to quantify both soil CO2 and CH4 emissions as well as crop performance under different tillage systems and N fertilization rates during three maize (Zea mays L.) growing seasons (2015–2017) in a semiarid area converted to irrigated. Three types of tillage (conventional tillage, CT, reduced tillage, RT, and no-tillage, NT) and three mineral N fertilization rates (0, 200, and 400 kg N ha−1) were compared in a randomized block design with three replications. Weekly soil CO2 and CH4 emissions, soil temperature and gravimetric moisture were measured. Moreover, maize above-ground biomass, grain yield, and above-ground C-inputs were quantified. Carbon dioxide emissions ranged from 173 to 4378 mg CO2-C m-2 d-1. No-tillage showed a greater mean soil CO2 flux than CT when applying the highest rate of N (400 kg N ha-1). Although some emissions of CH4 were observed, all treatments acted as net CH4 sinks during most of the experimental period. A linear multiple relationship between soil CO2 fluxes and soil gravimetric moisture (0–5 cm depth) and temperature (10 cm depth) were found. In the 2015 growing season, greater cumulative CO2 emissions were found under NT and RT compared with CT, while in 2016 N T showed the highest values compared to CT with intermediate values in RT. Differently, in 2017 no differences between tillage systems were found. When applying N fertilizer, NT and RT increased maize grain production and above-ground C-inputs compared to CT, since a severe soil crusting occurred in this last, which caused crop water deficit. The results suggest that tillage intensity and N fertilization rate reduction can increase maize biomass production and yield which leads to greater C-input that returns to the soil.