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Growing season drought can be devastating to crop yields. Soil microbial communities have the potential to buffer yield loss under drought through increasing plant drought tolerance and soil water retention. Microbial inoculation on agricultural fields has been shown to increase plant growth, but few studies have examined the impact of microbial inoculation on plant and soil microbial drought tolerance. We conducted a rainout shelter experiment and subsequent greenhouse experiment to explore 3 objectives. First, we evaluated the performance of a large rainout shelter design for studying drought in agricultural fields. Second, we tested how crop (corn vs. soybean) and microbial inoculation alter the response of soil microbial composition, diversity, and biomass to drought. Third, we tested whether field inoculation treatments and drought exposure altered microbial communities in ways that promote plant drought tolerance in future generations. In our field experiment, the effects of drought on soil bacterial composition depended on crop type, while drought decreased bacterial diversity in corn plots and drought decreased microbial biomass carbon in soybean plots. Microbial inoculation did not alter overall microbial community composition, plant growth, or drought tolerance despite our efforts to address common barriers to inoculation success. Still, a history of inoculation affected growth of future plant generations in the greenhouse. Our study demonstrates the importance of plant species in shaping microbial community responses to drought and the importance of legacy effects of microbial inoculation.