The co-occurrence of aflatoxin B1 (AFB1) and zearalenone (ZEN) in grain-based food and animal feed poses significant health risks to humans and animals due to their potent mutagenic, cytotoxic, and carcinogenic properties. Conventional physical and chemical methods are insufficient for effectively detoxifying multiple mycotoxins present in food and feed. In this study, we evaluated the capability of Bacillus subtilis ZJ-2019-1 (B. subtilis ZJ-2019-1) to simultaneously degrade AFB1 and ZEN while optimizing reaction to enhance degradation efficiency. The localization of active ingredients from B. subtilis ZJ-2019-1 was determined using high-performance liquid chromatography (HPLC). Our findings demonstrated that B. subtilis ZJ-2019-1 eliminated 60.88% of AFB1 and 33.18% of ZEN within 72 h at a concentration of 10 mg/L at 37 °C (pH 7.0) and exerted greater activity under alkaline conditions. The autoclaved and boiled supernatants of B. subtilis ZJ-2019-1 exhibited significant enhancement in the degradation of AFB1 and ZEN, achieving degradation rates of 79.85% and 100%, respectively, at a concentration of 1 mg/L within 48 h at 37 °C. Moreover, the crude enzymes from B. subtilis ZJ-2019-1 showed maximum degradation rates for AFB1 (100%) and ZEN (94.29%) within 72 h at 70 °C. Additionally, divalent cations (such as Co2+, Fe2+, Mn2+, and Ni2+) significantly augmented the activity of crude enzymes from B. subtilis ZJ-2019-1 towards mycotoxin degradation. Furthermore, when applied to corn gluten meals, B. subtilis ZJ-2019-1 strain effectively detoxify 66.08% of AFB1 and 22.01% of ZEN, surpassing the efficacy of a commercial detoxification agent on the market (34.17% for AFB1 and 2.28% for ZEN). Collectively, these findings indicated that B. subtilis ZJ-2019-1 is a promising candidate for the simultaneous removal of multiple mycotoxins in food and feed, while addressing health concerns associated with harmful mycotoxins.