ABSTRACT Droughts affect soil microbial abundance and functions—key parameters of plant–soil carbon (C) allocation dynamics. However, the impact of drought may be modified by the mean climatic conditions to which the soil microbiome has previously been exposed. In a future warmer and drier world, effects of drought may therefore differ from those observed in studies that simulate drought under current climatic conditions. To investigate this, we used the field experiment ‘Hohenheim Climate Change,’ an arable field where predicted drier and warmer mean climatic conditions had been simulated for 12 years. In April 2021, we exposed this agroecosystem to 8 weeks of drought with subsequent rewetting. Before drought, at peak drought, and after rewetting, we pulse‐labelled winter wheat in situ with 13 CO 2 to trace recently assimilated C from plants to soil microorganisms and back to the atmosphere. Severe drought decreased soil respiration (−35%) and abundance of gram‐positive bacteria (−15%) but had no effect on gram‐negative bacteria, fungi, and total microbial biomass C. This pattern was not affected by the mean precipitation regime to which the microbes had been pre‐exposed. Reduced mean precipitation had, however, a legacy effect by decreasing the proportion of recently assimilated C allocated to the microbial biomass C pool (−50%). Apart from that, continuous soil warming was an important driver of C fluxes throughout our experiment, increasing plant biomass, root sugar concentration, labile C, and respiration. Warming also shifted microorganisms toward utilizing soil organic matter as a C source instead of recently assimilated compounds. Our study found that moderate shifts in mean precipitation patterns can impose a legacy on how plant‐derived C is allocated in the microbial biomass of a temperate agroecosystem during drought. The overarching effect of soil warming, however, suggests that how temperate agroecosystems respond to drought will mainly be affected by future temperature increases.