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Surface drip fertigation has demonstrated promising results regarding the mitigation of nitrous oxide (N2O) emissions. The use of subsurface irrigation may offer the possibility of reducing these emissions further due to the modification of the soil moisture profile and N allocation, both of which affect the biochemical processes leading to N2O fluxes. However, the mitigation potential of subsurface irrigation combined with different mineral nitrogen (N) fertilizers (ammonium or nitrate-based, use of nitrification inhibitors) still needs to be evaluated. To respond to this need, a 2-year field experiment was set up in central Spain to test two different drip-fertigation systems (surface and subsurface at 30 cm depth) and four N fertilization treatments (control, calcium nitrate, and ammonium sulfate with or without the nitrification inhibitor 3,4-dimethylpyrazole phosphate, DMPP) in an irrigated maize (Zea mays L.) crop. Nitrous oxide emissions, mineral N concentrations (ammonium, NH4+, and nitrate, NO3−), and abundance of key N genes involved in nitrification and denitrification processes were measured in two soil layers (0–20 and 20–40 cm). Regardless of the irrigation system, ammonium sulfate gave the highest cumulative N2O losses in both campaigns, while calcium nitrate and the use of DMPP were the most effective strategies to abate N2O fluxes in the first and second years, respectively. Differences between irrigation systems were not statistically significant for cumulative N2O emissions, despite the clear effect on topsoil mineral N (higher NH4+ and NO3− concentrations in surface and subsurface drip, respectively). Nitrous oxide emissions were positively correlated with soil NH4+ concentrations. Gene abundances were not a trustworthy predictor of N2O losses in the 1st year, although a clear inhibitory effect of fertilization on microbial communities (i.e., ammonia oxidizers, nitrite reducers, and N2O reducers) was observed during this campaign. During the second year, nitrifying and denitrifying genes were affected by irrigation (with higher abundances in the 20–40 cm layer in subsurface than in surface drip) and by the addition of DMPP (which had a detrimental effect on gene abundances in both irrigation systems that disappeared after the fertigation period). In conclusion, the use of DMPP or calcium nitrate instead of ammonium sulfate may enhance the chances for an additional mitigation in both surface and subsurface irrigation systems. [ABSTRACT FROM AUTHOR]