The impacts of climate change, such as drought, can affect soil microbial communities. These communities are crucial for soil functioning and crop production. Organic and conventional cropping systems can promote distinct soil microbiomes and soil organic carbon contents, which might generate different capacities to mitigate drought effects on these cropping systems. A field-scale drought simulation was performed in long-term organically and conventionally managed cropping systems differing in fertilization and pesticide application. The soil microbiome was assessed during and after drought in bulk soil, rhizosphere, and roots of wheat. We found that drought reduced soil respiration and altered microbial community structures, affecting fungi in the bulk soil and rhizosphere more strongly than prokaryotes. Microbial communities associated with crops (i.e. rhizosphere and root) were more strongly influenced by drought compared to bulk soil communities. Drought legacy effects were observed in the bulk soil after harvesting and rewetting. The extent of the structural shifts in the soil microbiome in response to severe drought did not differ significantly between the organic and conventional cropping systems but each cropping system maintained a unique microbiome under drought. All cropping systems showed relative increases in potential plant growth-promoting genera under drought but some genera such as Streptomyces, Rhizophagus, Actinomadura, and Aneurinibacillus showed system-specific drought responses. This agricultural field study indicated that fungal communities might be less resistant to drought than prokaryotic communities in cropping systems and these effects get more pronounced in closer association with plants. Organic fertilization and the associated increase in soil organic carbon, or the reduction in pesticide application might not have the proposed ability to buffer severe drought stress on soil microbial taxonomic diversity. Yet, it remains to be elucidated whether the ability to maintain system-specific soil microbiomes also during drought translates into different functional capabilities to cope with the stress.