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Plant-associated microbes contribute to crop health and resilience, potentially extending or complementing plant traits under abiotic stress. Here we tested a series of hypotheses centered on the fungal mycobiome and bacterial microbiome of field-grown sorghum (Sorghum bicolor), an emerging model crop for drought resilience, which we cultivated under arid conditions. Overall, the sorghum mycobiome and microbiome differed in composition between the exterior and interior of plant tissues, between roots and leaves, and among sorghum genotypes. We did not observe variation in fungal and bacterial endophytes among performance classes of sorghum when water was plentiful, but the root endophytic mycobiome and microbiome both shifted markedly under water limitation, with similar shifts in composition observed among multiple plant genotypes. The root endophytic microbiome of high-performing sorghum was especially responsive to water limitation. Network analysis suggested that water limitation did not directly remodel these root endophytic microbiomes, such that interactions of the microbiome with the host plant, rather than interactions among microbes within the microbiome, may be the most dynamic element of change when water is limited. Overall, our study points to shifts in the prevalence of particular taxa under abiotic stress and suggests that high-performing lines may have distinctive features as substrates or strategies for actively recruiting diverse, abundant, and distinctive microbial communities to roots under water limitation. Such findings are important in the arid lands that frame marginal agriculture today and comprise an increasing proportion of agriculture in a changing world.