Pesticides are key stressors of soil microorganisms with reciprocal effects on ecosystem functioning. These effects have been mainly attributed to the parent compounds, while the impact of their transformation products (TPs) has been largely overlooked. We assessed, in a meadow soil (A),the transformation of iprodione and its toxicity on the (i) abundance of functional microbial groups, (ii) activity of key microbial enzymes and (iii) diversity of bacteria, fungi and ammonia-oxidizing microorganisms (AOM) using amplicon sequencing. 3,5-Dichloroaniline (3,5-DCA), the main iprodione TP, was identified as key explanatory factor for the persistent reduction in enzymatic activities and potential nitrification (PN), and for the observed structural changes in the bacterial and fungal community. The abundance of certain bacterial (, , and ) and fungal () groups were negatively correlated with 3,5-DCA. A subsequent study in a fallow agricultural soil (B) showed a limited formation of 3,5-DCA which concurred with the lack of effects on nitrification. Direct 3,5-DCA application in soil B induced a dose-dependent reduction of PN and NO-N, which recovered with time. assays with terrestrial AOM verified the greater toxicity of 3,5-DCA over iprodione. Nitrosotalea sinensis Nd2 was the most sensitive AOM to both compounds. Our findings build on previous evidence on the sensitivity of AOM to pesticides reinforcing their potential utilization as indicators of the soil microbial toxicity of pesticides in pesticide environmental risk analysis and stressing the need to consider the contribution of TPs in the toxicity of pesticides on the soil microbial community. Pesticide toxicity on soil microorganisms is an emerging issue in pesticide risk assessment, dictated by the pivotal role of soil microorganisms on ecosystem services. However, the focus has traditionally been on parent compounds, while transformation products (TPs) are largely overlooked. We tested the hypothesis that TPs can be major contributors on the soil microbial toxicity of pesticides, using, iprodione, and its main TP, 3,5-dichloroaniline, as model compounds. We demonstrated, by measuring functional and structural endpoints, that 3,5-dichloraniline and not iprodione was associated with adverse effects on soil microorganisms, with nitrification being mostly affected. Pioneering assays with relevant ammonia-oxidizing bacteria and archaea verified the greater toxicity of 3,5-dichloraniline. Our findings are expected to advance environmental risk assessment highlighting the potential of ammonia-oxidizing microorganisms as indicators of the soil microbial toxicity of pesticides and stressing the need to consider the contribution of TPs on pesticides soil microbial toxicity.