An aerobic 15 N microcosmic experiment was conducted to compare the inhibitory effects of the biological nitrification inhibitor (BNI), methyl 3-(4-hydroxyphenyl) propionate (MHPP) at rates of 500 and 1000 mg kg −1 with the synthetic nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) at 1% of applied NH 4 + , on the gross nitrification rate ( n _gross ) and on the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) of two contrasting soils (pH: 5.10 vs. 8.15, clay content 17.8 vs. 30.8). DMPP inhibited 56.6% of n _gross in the acidic soil and 50.3% in the calcareous soil, whereas MHPP inhibited 18.3–55.5% of n _gross in the acidic soil and 14.1–20.2% in the calcareous soil. MHPP used at the high rate showed the same inhibition on n _gross as DMPP in the acidic soil but not in the calcareous soil. DMPP and MHPP likely regulated n _gross by causing niche differentiation between AOA and AOB. Moreover, the community composition of AOB was more sensitive to nitrification inhibitor application than that of AOA, particularly in the acidic soil. However, the response of AOB community composition was less sensitive to the application of MHPP than to that of DMPP. MHPP mainly targeted Nitrosospira clusters 3a.2, 3b.2, and 9 of the AOB in the acidic soil.