<p>The rapid advancements in science and technology have significantly increased the demand for lithium, rubidium, and cesium. However, the limited natural availability of these metals underscores the need to explore secondary resources for their recovery. This study investigates the extraction of lithium, rubidium, and cesium from boron waste using bioleaching with <i>Bacillus licheniformis</i> (<i>B. licheniformis</i>). A three-factor, three-level Box–Behnken design (BBD), combined with response surface methodology (RSM), was employed to evaluate the effects and interactions of key parameters on metal extraction efficiency. The independent variables included the liquid/solid (L/S) rate (50–200 mLg⁻¹), temperature (20–40&#xa0;°C), and bioleaching time (10–30&#xa0;days). The model predicted optimal extraction yields of 11.24% for Li, 45.86% for Rb, and 27.36% for Cs under the conditions of 20&#xa0;days, 30&#xa0;°C, and an L/S rate of 125 mLg⁻¹.</p><p>This study is noteworthy for reducing the environmental impact of industrial waste by repurposing it as a valuable resource, while also enabling the economic recovery of critical metals. Furthermore, it contributes to the existing body of research by highlighting the bioleaching potential and mechanism of <i>B. licheniformis</i> in the treatment of boron waste.</p> Graphic Abstract <p></p>