Green pesticides are highly desirable, as they are environmentally friendly and efficient. In this study, the antifungal peptide P852 was employed to suppress Fusarium wilt in the Faba bean. The disease index and a range of physiological and metabolomic analyses were performed to explore the interactions between P852 and the fungal disease. The incidence and disease index of Fusarium wilt were substantially decreased in diseased Faba beans that were treated with two different concentrations of P852 in both the climate chamber and field trial. For the first time, P852 exhibited potent antifungal effects on Fusarium in an open field condition. To explore the mechanisms that underlie P852′s antifungal effects, P852 treatment was found to significantly enhance antioxidant enzyme capacities including guaiacol peroxidase (POD), superoxide dismutase (SOD), catalase (CAT), and the activities of antifungal enzymes including chitinase and β-1,3-glucanase, as well as plant dry and fresh weights, and chlorophyll content compared to the control group (p ≤ 0.05). Metabolomics analysis of the diseased Faba bean treated with P852 showed changes in the TCA cycle, biological pathways, and many primary and secondary metabolites. The Faba bean treated with a low concentration of P852 (1 μg/mL, IC50) led to upregulated arginine and isoquinoline alkaloid biosynthesis, whereas those treated with a high concentration of P852 (10 μg/mL, MFC) exhibited enhanced betaine and arginine accumulation. Taken together, these findings suggest that P852 induces plant tolerance under Fusarium attack by enhancing the activities of antioxidant and antifungal enzymes, and restoring plant growth and development.