Continuous cropping severely affects faba bean growth, mainly due to pathogen and autotoxic substance accumulation. Here, we used faba bean monocropping (M) and intercropping with wheat (I), with stress treatments of Fusarium oxysporum f. sp. fabae (FOF) alone (F) and combined with cinnamic acid (F + C), to analyze seedling growth, defense‐related enzymes, levels of resistance‐associated substances, and protein expression profiles in roots. The results showed that intercropping mitigated the inhibitory effects of FOF and cinnamic acid. FOF resulted in increased activities of defense‐related enzymes as well as levels of resistance‐associated substances. Proteomic analysis showed that 22 proteins were upregulated following FOF inoculation (M + F), and 6 proteins were downregulated after the addition of cinnamic acid (M + F + C) in monocropping plants; these proteins were mainly involved in pathways associated with carbohydrate metabolism, energy, and the cytoplasm. Comparison of monocropping and intercropping indicated that the upregulated proteins were mostly associated with stress and defense, carbohydrate transport and metabolism, maintenance of cellular homeostasis, and protein synthesis. KEGG analysis revealed that intercropping increased enrichment in pathways associated with metabolism, ribosomes, biosynthesis of secondary metabolites, proteasomes, pyruvate metabolism, and pentose and glucuronate interconversions. The results indicated that intercropping mitigated growth inhibition by FOF and cinnamic acid by increasing energy production, maintaining normal cellular functions, and promoting the synthesis of defense‐associated secondary metabolites. These findings provide a basis for further investigation into the molecular mechanisms underlying the effects of intercropping in controlling resistance to Fusarium wilt in the faba bean.