This study evaluated the effects of nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) and fungicide iprodione on net nitrification rates and abundances of functional genes related to nitrification and denitrification in an agricultural soil. Single DMPP application or repeated iprodione applications decreased net nitrification rates in the test soil. However, when the DMPP and iprodione were applied together, they could generate antagonistic effects on the inhibitions of net nitrification rates. Repeated iprodione applications reduced ammonia-oxidizing archaea and bacteria (AOA and AOB) amoA gene abundances, while DMPP application decreased AOB amoA gene abundances only. The abundances of narG and nirK genes were negatively affected by repeated iprodione applications. Our results demonstrated that combined applications of DMPP and iprodione could generate antagonistic effects on the inhibitions of net nitrification rates and discrepant impacts on the abundances of functional genes related to soil denitrification