Acid mine drainage (AMD), a common environmental problem around the world, is characterized by low pH, high concentrations of heavy metals and sulfate. AMD treatment technology based on stimulating in-situ microorganisms has received widespread attention, but lack of organic matter is a limiting factor that restricts the remediation by heterotrophic microorganisms such as sulfate-reducing bacteria (SRB). In this study, a pilot scale reactor was set up next to an acid reservoir to evaluate the effect of livestock wastes on the in-situ bioremediation of AMD, focusing on performance assessment, heavy metal removal efficacy, and the evolution of the microbial community. Results indicated that the pH of AMD rises rapidly from 3.23 to 4.11, and metals (e.g., Fe, Cu, and Zn) rapidly got removed in Stage I. However, AMD experienced significant stratification in Stage Ⅱ (biogas slurry supplemented). The pH of surface layer (0.5 m below the surface) gradually dropped to 3.67, and the bottom layer (2.3 m below the surface) remained around 4.1, and the metal removal efficiencies further improved. Microbial communities were dominated by Fe-OB and Fe-RB in surface layer, while SRB dominated in bottom layer. The addition of biogas slurry significantly increased the relative abundance of functional microbe in bioremediation. The growth of SRB in the bottom of the reactor made an important contribution to heavy metal removal. Heavy metals were mainly removed through the formation of insoluble hydroxide and sulfide precipitation and co-precipitation. This study innovatively integrates low-cost, locally sourced livestock waste as nutrient supplements into AMD bioremediation processes, and demonstrated the potential for integrating AMD treatment with livestock waste management, addressing both the nutrient needs for AMD processing and the challenge of livestock waste disposal. The findings contribute to the development of cost-effective and eco-friendly strategies for AMD management while advancing the understanding of microbial mechanisms of in-situ bioremediation.