Aims <p>Banana Fusarium wilt disease severely threatens the sustainable development of the banana industry. Regulating the local microbiome to reduce disease incidence offers broader adaptability, with a potential exploration into plant-induced recruitment of beneficial microbes. Our previous study showed that the plant elicitor Isotianil induces resistance to banana Fusarium wilt. This study assessed the impact of Isotianil on soil microbiomes.</p> Methods <p>Pot experiments were conducted with the susceptible banana cultivar Baxijiao and the tolerant cultivar Yunjiao No. 1, inoculating them with the Fusarium pathogen and introducing Isotianil by foliar application and root drenching. Amplicon sequencing was used to analyze the rhizosphere bacterial and fungal communities.</p> Results <p>Results showed that Isotianil had 48% and 55% disease control efficacy rates for Baxijiao and Yunjiao No. 1 after foliar application, and 51% and 55% after root drenching, respectively. Amplicon sequencing revealed that, compared to pathogen alone, foliar application of Isotianil significantly altered the bacterial and fungal community compositions in Yunjiao No. 1, while root drenching significantly changed these communities in both cultivars. Root drenching of Isotianil notably increased the relative abundance of potential beneficial microbes such as <i>Blrii41</i>, <i>Devosia</i>, and <i>Acremonium</i> and enhanced the stability of bacterial and fungal cross-kingdom networks. Additionally, the application of Isotianil increases the impact of stochastic processes in the bacterial community assembly of Baxijiao while decreasing their importance in Yunjiao No.1.</p> Conclusions <p>These findings suggest that Isotianil application modulates the rhizosphere microbiome, promoting beneficial microbes, stabilizing microbial networks, potentially contributing to disease suppression.</p>