Mine waste disposal in dumps and stockpiles causes environmental pollution, particularly through microbe-assisted acid mine drainage (AMD) generation and groundwater contamination with hazardous heavy metal(loid)s. Metal hyper-resistance in acidophilic microorganisms remains an underexplored intriguing phenomenon. Using a multi-level approach, we provide the first data on extreme zinc resistance mechanisms in Sulfobacillus thermotolerans, recognized as one of the most metal-resistant organisms known. Under high zinc levels, Sb. thermotolerans cells exhibited efficient zinc sorption and low intracellular accumulation. Remarkably, mechanisms involved the upregulation of stress response and metabolic pathway proteins, including different GroEL chaperonin forms. Moreover, overexpression of the Sb. thermotolerans StGroEL chaperonin in Escherichia coli enhanced its growth and zinc resistance under zinc stress. 3D structure modeling and ion binding site prediction in StGroEL revealed 46 amino acid residues potentially involved in zinc docking. Thriving in natural and engineered environments, such as sulfide mines, mine waste disposal sites, and AMD, Sb. thermotolerans is a key member of acidophilic microbial communities used in commercial biotechnologies for sulfidic raw material processing. These findings, beyond their fundamental scientific relevance, have important implications for environmental protection, including AMD management, safe hazardous waste disposal, and a broader application of eco-friendly biomining technologies using metal-resistant microbial communities.