Fertilization with micronutrients (e.g., zinc, Zn) is essential in order to overcome the global nutritional problems associated with human micronutrient deficiencies. However, little is known about the effect of micronutrient fertilizers and their interaction with nitrogen (N) on greenhouse gas (GHG) emissions and soil microbial processes involved in nitrous oxide (N2O) fluxes. In this context, a one-year field experiment was carried out using a winter wheat (Triticum aestivum L) crop in Central Spain. Winter wheat was treated with different Zn sources (Zn-sulphate, Zn-lignosulphonate, Zn with a mixture of synthetic chelating compounds DTPA-HEDTA-EDTA and Zn-humic/fulvic acids) and N rates (0, 120 and 180 kg N ha(-1)). Zn sources were applied at 10 kg Zn ha(-1) for Zn-sulphate and 0.36 kg Zn ha(-1 )for the rest of treatments. Nitrous oxide, methane (CH4) and respiration fluxes were measured (two-three times per week during the first month after each fertilization and thereafter with decreasing frequency), as were the total abundances of soil Bacteria and Archaea, ammonia-oxidizing Bacteria and Archaea, and denitrifying bacteria. The DTPA-HEDTA-EDTA reduced cumulative N2O losses by 21.4% and respiration fluxes by 24.4% from those of the no Zn application. The chelating of metal co-factors (mainly copper, Cu) of the enzymes involved in the nitrification and denitrification steps was the probable mechanism for the reduction of N2O emissions as bacterial amoA, nit-K, nirS and norB gene abundances, as well as the extractable Cu content, decreased in this treatment. Unexpectedly, the DTPA-HEDTA-EDTA increased the copy number of nosZ by 31.2% over that of the no Zn application. The Zn applied together with the humic/fulvic acids mixture caused significant increases of total bacterial abundance and nitrifier and denitrifier communities, particularly the norB gene, thereby leading to the highest N2O emissions. The optimum N rate was 120 kg N ha(-1) since it resulted in the lowest yield-scaled N2O losses and N surplus. The application of synthetic Zn chelates can be recommended as a win-win mitigation and adaptation strategy aimed at reducing yield-scaled GHG emissions and at the enhancement of Zn biofortification.