Soil microorganisms have a pivotal role in ecosystem functioning. In 2010, EFSA identified soil microorganisms as a specific protection goal for environmental risk assessment of pesticides. Despite that, the assessment of the soil microbial toxicity of pesticides still relies on an out-of-date N transformation test overlooking the recent methodological and standardization advances in soil microbial ecology. Within the frame of two EU-funded projects (ECOFUN-MICROBIODIV& LOVE-TO-HATE) we developed a toolbox of ISO standardized and of new methods which enable the comprehensive assessment of the toxicity of pesticides on soil microorganisms following a tiered experimental approach. This involved pesticide testing against natural microbial assemblages,initially at laboratory-scale under high exposure conditions, followed by field-scale assessment under more realistic exposure scenarios. In 2017EFSA proposed the use of arbuscular mycorrhizal fungi (AMF) as one of the possible bioindicators to assess the soil microbial toxicity of pesticides. Mounting evidence suggest that ammonia-oxidizing microbes (AOM) constitute another could also serve asbioindicatorssince (a) they are sensitive to external disturbances including pesticides, (b) they mediate the rate-limiting step of N cycle and (c) there are ISOstandardized tools to measure their activity and abundance. Key experimental aspects of the scheme proposed are (a) the parallel determination of the dissipation and metabolism of pesticides to allow the identification of the compound (parent or metabolite) responsible for toxicity effects observed, (b) the duration of the tests should allow microbial recovery, (c) effects on microbial diversity, although powerful tools are now available their application is still far from standardized. The proposed tiered scheme could be augmented with an in vitro assessment step on representative AOMs and AMF as an initial conservative tierbefore testing against natural soil assemblages. However, certain aspects of in vitro testing require further development standardization. Acknowledgements : This work was funded in the frame of the IAPP-FP7-MSCA project LOVE-TO-HATE