This study investigated the potential application of a microorganism-derived biocoagulant based on the bacterial strain Acidithiobacillus ferrooxidans Ach1 to improve the treatment efficiency of wastewater containing organic pollutants. The relevance of the study is associated with the high level of organic and petroleum contamination of wastewater in Kazakhstan, including Shymkent, and the need to improve conventional wastewater treatment technologies. Municipal wastewater from Shymkent was used as the research object. The A. ferrooxidans Ach1 strain was isolated from polymetallic slags and cultivated in Silverman–Lundgren 9K nutrient medium. During microbial cultivation, Fe²⁺ ions were oxidized to Fe³⁺, resulting in the biological formation of ferric sulfate, which served as the basis for the microorganism-derived biocoagulant. The main physicochemical characteristics of the wastewater, including chemical oxygen demand (COD), biochemical oxygen demand (BOD₅), phosphates, petroleum products, and oils, were determined. The results showed that the concentrations of COD, phosphates, petroleum products, and oils in the municipal wastewater exceeded the permissible levels. Based on the experimental findings, a technological scheme integrating mechanical, biocoagulation, and biological treatment stages was proposed. The developed technology has the potential to partially or completely replace conventional chemical coagulants, reduce chemical reagent consumption, and improve the environmental sustainability of wastewater treatment. The findings demonstrate the scientific and practical potential of A. ferrooxidans Ach1-derived biocoagulation for the treatment of organic wastewater.