Acid mine drainage originates from metal sulfides oxidation, which results in acidic metal-rich leachate. In this study, a novel and environmentally friendly approach was demonstrated to passivate pyrite and lead-zinc tailings, respectively. The key to this approach is to develop biofilms of the marine bacterium Qipengyuania flava S1. Biofilms can induce biomineralization, thereby isolating metal sulfides from air and water. The stability and biological toxicity of the bio-passivation layers were evaluated by leaching bio-passivated pyrite or tailings in initially acidic H2O2 solutions with shaking for 180 days and then cultivating Brassica chinensis and Allium cepa with the leachates. Our results showed that after passivation, the amount of iron released by pyrite decreased by at least 99.2 ± 0.2 (in wt%). For lead-zinc tailings after passivation, the released metal ions (Fe+Al+Pb+Zn) decreased by at least 52.0 ± 3.2 (in wt%). The bio-passivation layers also maintained the pH of the leachate in the range of 7.5–8.0. Before bio-passivation, compared with mineral water, the pyrite leachate significantly inhibited the growth of the two plants, and the tailings leachate significantly inhibited the growth of A. cepa, whereas the bio-passivated pyrite or tailings leachate did not show any inhibitory effect.