The nitrification inhibitor, 3,4-dimethylpyrazol-phosphate (DMPP) and the urease inhibitor N-(n-butyl) thiophosphoric triamide (nBTPT) can mitigate N losses through reducing nitrification and ammonia volatilization, respectively. However, the impact of repeated applications of these inhibitors on nitrogen cycling microorganisms is not well documented. This study aimed to investigate the changes in the abundance and community structure of the functional microorganisms involved in nitrification and denitrification in Australian pasture soils after repeated applications of DMPP and nBTPT.Materials and methods Soil was collected in autumn and spring, 2014 from two pasture sites where control, urea, urea ammonium nitrate, and urea coated inhibitors had been repeatedly applied over two years. Soil samples were analyzed to determine the potential nitrification rates (PNRs), the abundances of amoA, narG, nirK and bacterial 16S rRNA genes, and the community structure of ammonia oxidizers.Results and discussion Two years of urea application resulted in a significantly lower soil pH at Terang and a significant decrease in total bacterial 16S rRNA gene abundance at Glenormiston, and led to significantly higher PNRs and abundances of ammonia oxidizers compared to the control. Amendment with either DMPP or nBTPT significantly decreased PNRs and the abundance of amoA and narG genes. However, there was no fertilizer-or inhibitor-induced change in the community structure of ammonia oxidizers.Conclusions These results suggest that there were inhibitory effects of DMPP and nBTPT on the functional groups mediating nitrification and denitrification, while no significant impact on the community structure of ammonia oxidizers was observed. The application of nitrification or urease inhibitor appears to be an effective approach targeting specific microbial groups with minimal effects on soil pH and the total bacterial abundance. Keywords 3,4-dimethylpyrazole phosphate (DMPP) • Ammonia-oxidizing archaea • Ammonia-oxidizing bacteria • N-(n-butyl) thiophosphoric triamide (nBTPT)