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Drought and agricultural management influence soil microorganisms with unknown consequences for the functioning ofagroecosystems. We simulated drought periods in organic (biodynamic) and conventional wheat fields and monitoredeffects on soil water content, microorganisms and crops. Above the wilting point, water content and microbial respirationwere higher under biodynamic than conventional farming. Highest bacterial and fungal abundances were found inbiodynamically managed soils, and distinct microbial communities characterised the farming systems. Most biological soilquality parameters and crop yields were only marginally affected by the experimental drought, except for arbuscularmycorrhizal fungi (AMF), which increased in abundance under the experimental drought in both farming systems. AMFwere further strongly promoted by biodynamic farming resulting in almost three times higher AMF abundance underexperimental drought in the biodynamic compared with the conventional farming system. Our data suggest an improvedwater storage capacity under biodynamic farming and confirms positive effects of biodynamic farming on biological soilquality. The interactive effects of the farming system and drought may further be investigated under more substantialdroughts. Given the importance of AMF for the plant’s water supply, more in-depth studies on AMF may help to clarify theirrole for yields under conditions predicted by future climate scenarios.