Previous studies have shown that the use of zinc (Zn) chelate fertilizers combined with a nitrogen (N) fertilizer (urea) can lead to both agronomic (i.e., yields and Zn and N biofortification due to the synergies between both nutrients) and environmental (i.e., by reducing the emissions of nitrous oxide, N2O, derived from N fertilization) benefits under rainfed semi-arid conditions. However, little is known about the effect of Zn-N co-fertilization on greenhouse gas (GHG) emissions or soil microbial processes involved in N2O fluxes under non-flooded irrigated conditions (during the dry season). Under these conditions, water-filled pore space continuously fluctuates following a periodic pattern and soil temperatures are in the optimum range for soil microorganisms. In this context, a field experiment was conducted using a maize (Zea mays L.) crop treated with two N levels (no N application and 120 kg N ha−1 as urea), and three Zn sources (no Zn application, Zn sulphate, and Zn applied with a mixture of chelating compounds, DTPA-HEDTA-EDTA). Nitrous oxide, methane (CH4) and carbon dioxide (CO2) fluxes were measured using opaque chambers, as well as the total abundances of soil bacteria, archaea and nitrifier and denitrifier communities. Zn-N co-fertilization increased cumulative N2O emissions from 0.36 kg N-N2O ha−1 (for urea combined with Zn chelates) to 0.76 kg N-N2O ha−1 (for urea combined with Zn sulphate), with respect to urea without Zn application. The N2O emission factors were lower (0.34%–0.72%) than the IPCC default value of 1%. Total abundances of the nosZ denitrification gene, which is involved in the reduction in N2O to dinitrogen (N2), were reduced by 75% on average in the plots that received Zn fertilizers. This reduction may explain the higher N2O emissions in these treatments. In contrast with the case with non-irrigated crops, Zn-N co-fertilization cannot be recommended as a strategy to mitigate N2O emissions in irrigated maize under semi-arid conditions, despite of the enhancement of Zn availability in soil.