Colletotrichum capsici is the etiological agent of Capsicum anthracnose. Bacillus velezensis has traditionally been recognized as an effective biocontrol agent; however, its efficacy decreases due to soil acidification. In this study, we domesticated Bacillus velezensis XY40-1 along an acid resistance gradient, resulting in a strain capable of growth at pH 4, and might adapt to acidic environments by regulating genes related to spore formation. Notably, the domesticated Bacillus velezensis XY40-1 exhibits significant antagonistic activity against Colletotrichum capsici in acidic dual cultures and effectively reduces the disease index in Capsicum. The domesticated strain employs a direct antifungal strategy under acidic conditions, with the production of amylocyclicin, regulated by acnA, potentially serving as a primary mechanism through which Bacillus velezensis combats Colletotrichum capsici. Conversely, under neutral conditions, domesticated Bacillus velezensis focuses on bolstering its defense mechanisms by increasing the expression of katA, ahpF, and ahpC genes to detoxify peroxides. In addition, a dual RNA-Seq analysis comprehensively investigated the acid tolerance mechanisms and defensive responses of B. velezensis and the pathogenic mechanisms of C. capsici, providing a foundation for the practical application of B. velezensis as a biocontrol agent. These findings offer important insights into the impact of soil acidification on plant disease suppression and contribute to the development of sustainable agricultural practices. IMPORTANCE: Recently, the increasing issue of soil acidification has worsened anthracnose disease in Capsicum, caused by Colletotrichum capsici. Our study demonstrated that Bacillus velezensis can effectively inhibit the growth of Colletotrichum capsici. However, the molecular mechanisms underlying the interaction between Bacillus velezensis and Colletotrichum capsici remain largely unexplored. Here, we developed an interaction system between Bacillus velezensis and Colletotrichum capsici to explore their dynamic relationship. By employing dual RNA-Seq methods, we were able to comprehensively investigate the acid tolerance mechanisms and defense responses of Bacillus velezensis, alongside the pathogenic mechanisms of Colletotrichum capsici. This establishes the groundwork for utilizing Bacillus velezensis as an effective biocontrol agent in agriculture.