Domestication and intensive management practices have significantly shaped characteristics of modern crops. However, our understanding of domestication’s impact had mainly focused on aboveground plant traits, neglecting root and rhizospheric traits, as well as trait-trait interactions and root-microbial interactions. To address this knowledge gap, we grew modern ( Hordeum vulgare L. var. Barke) and wild barley ( H. spontaneum K. Koch var. spontaneum) in large rhizoboxes. We manipulated soil microbiome by comparing disturbed (sterilized soil inoculum, DSM) versus non-disturbed (non-sterilized inoculum, NSM) microbiome Results showed that modern barley grew faster and increased organic-carbon exudation (OC _EXU) compared to wild barley. Interestingly, both barley species exhibited accelerated root growth and enhanced OC _EXU under DSM, indicating their ability to partially compensate and exploit the soil resources independently of microbes if need be. Plant trait network analysis revealed that modern barley had a denser, larger, and less modular network than wild barley indicating domestication’s impact on trait coordination. Further, soil microbiome influenced specific network parameters. While the relative abundance of bacteria didn’t vary between wild and modern barley rhizospheres, species-specific core bacteria were identified, with stronger effects under DSM. Overall, our findings highlight domestication-driven shifts in root traits, trait coordination, and their modulation by the soil microbiome.