The accumulation of metal-containing waste, particularly lead and copper slags, presents a pressing environmental and economic issue in Kazakhstan. This study investigates bioleaching as a sustainable alternative to conventional extraction methods for recovering valuable metals from industrial waste. Metal-tolerant microorganisms, including Acidithiobacillus ferrooxidans, Nitrosomonas europaea, and micromycetes such as Aspergillus niger and Aspergillus flavus, were isolated and characterized to enhance bioleaching efficiency. Experiments using heap and tank leaching under controlled conditions examined key factors such as temperature, pH, particle size, and organic content. Bioleaching showed superior performance over sulfuric acid leaching, achieving recovery rates of 4.32 kg/t for copper and 14.91 kg/t for zinc. Optimal conditions were identified at +30 to +35 °C, pH 7–9, and particle sizes of 0.5–1.0 mm. Microscopic analysis confirmed that micromycetes contributed to metal dissolution by stabilizing pH and supporting microbial activity. The findings demonstrate that bioleaching is an effective, eco-friendly method that reduces the need for harsh chemicals while improving resource efficiency. The study supports further development of bioleaching technologies for industrial-scale applications.