Epichloë endophytes enhance plant defense and biotic stress resistance through mutualistic interactions in natural hosts. However, whether these protective effects are retained in annual non-native hosts such as barley (Hordeum vulgare L.) remains unclear. An integrated multi-omics approach was used to characterize defense responses in Epichloë bromicola-infected barley (LD1) and endophyte-free barley (CK) following pathogen challenge. The results show that LD1 had 20.0% lower disease incidence and 24.1% lower disease index than CK. LD1 also exhibited 21.1% lower malondialdehyde (MDA) content and higher antioxidant enzyme activities, indicating more effective control of oxidative damage and improved redox homeostasis. Integrated transcriptomic and metabolomic analyses revealed distinct defense responses between LD1 and CK. LD1 showed stronger activation of glutathione metabolism and antioxidant pathways than CK after 6 h of endophyte inoculation. This was consistent with more efficient control of early reactive oxygen species (ROS) dynamics. By 48 h, LD1 preferentially enriched phenylpropanoid biosynthesis and mitogen-activated protein kinase (MAPK) signaling, accompanied by increased accumulation of defense-related metabolites and enhanced structural and chemical defenses. Collectively, the study demonstrates that Epichloë bromicola enhances disease resistance in barley by reprogramming host defense dynamics from early redox regulation to late structural and chemical reinforcement.