BarleyMicroBreed builds on the paradigm that crop resource efficiency and stress resilience can be significantly improved by optimizing the capacity of plant roots to efficiently interact with the existing soil microbiota. We therefore propose to advance our mechanistic understanding of interactions between the crop plant genome, root phenotypic traits, and the root-associated microbiota to identify novel breeding strategies for crops tailored to harness the benefits of the indigenous soil microbial diversity. A holo-omics analysis of functionally annotated barley genomes together with a catalogue of root microbiota assemblages and phenotypic data including drought responses of 600 barley varieties determined in field trials in Austria, Lebanon and Morocco, will enable the identification of barley genome components, microbiota members and root traits important for drought resilience. Barley genome regions putatively important for microbiota assembly and drought resistance will be validated by gene knock-outs and causative effects will be explored using a combination of metabolomics, metagenomics and root phenotyping in pot and rhizobox experiments. To improve root phenotyping, we will develop tools including core break imaging systems, software developments for “gap filling” in rhizobox phenotyping, and models to infer seedling to mature root system architecture. Finally, with the knowledge of the genetic regulation of phenotypic root plasticity of barley lines we will implement strategies to create drought adaptive barley varieties with improved root systems and microbiomes. A selection of lines based on drought responses, microbiome assembly and root systems will be backcrossed into elite European lines and tested in field trials. We argue that breeding for crops tailored to harness the benefits of the indigenous soil microbial diversity rather than inoculating crops with plant-beneficial microorganisms will be a much more feasible and long-lasting strategy.