RationaleThe faba bean-wheat intercropping system is widely adopted to mitigate the incidence of faba bean wilt. The application of nitrogen fertilizers is imperative for promoting crop growth. Determining the optimal nitrogen dosage is crucial for enhancing the disease control efficacy of intercropping systems. So far, the impact of different nitrogen input management on soil microbial communities during the occurrence of faba bean diseases under intercropping conditions of faba bean and wheat has not been clear. ObjectiveTo explore the effect of different nitrogen application levels on the inter-root soil microbial community of faba bean in intercropping scenarios and its relationship with the incidence of faba bean wilt. Materials and methodsTwo planting modes, namely sole faba bean cultivation (M) and faba bean-wheat intercropping (I), were established in both field and pot experiments. Four nitrogen application levels (N0: 0 kg ha−1; N1: 45 kg ha−1; N2: 90 kg ha−1; and N3: 135 kg ha−1) were used to assess the incidence of wilt disease in faba bean. Furthermore, collect soil samples from the rhizosphere of faba bean plants for enzyme and microbial assays in the rhizosphere soil. ResultsThe application of nitrogen (N1, N2, and N3) reduced the incidence of faba bean wilt in the monocultures. Among the same N application levels, intercropping exhibited a significant decrease in wilt incidence compared with monocropping, with the lowest incidence observed at the N2 level. Additionally, the rhizosphere enzyme activity in faba bean was maximized under intercropping at the N2 level. Intercropping increased the richness and diversity of soil microorganisms, leading to an adjusted microbial community structure and the promotion of beneficial microorganism functions. Notably, nitrogen application played a pivotal role in changing the rhizosphere soil microbial community structure of faba bean. A reasonable nitrogen application rate (N2) can significantly improve the disease control effects of intercropping. ConclusionIntercropping with N2(90 kg ha−1) resulted in a significant increase in microbial diversity in faba bean soil. This led to an adaptable microbial structure, effectively mitigating the occurrence of faba bean wilt and ultimately promoting soil function and health.