<p>Chalcopyrite is often associated with manganese- and iron-rich minerals in nature. However, both iron and manganese have direct and substantial effects on the solvent extraction (SX), stripping and electrowinning processes for copper. The situation becomes intricate in occurrence of substantial concentration of silica from copper solvent extraction. Hence, the mitigation strategies for the two components (Fe and Mn) within the copper bioleaching solution in the presence of silica are crucial for achieving optimal results in the solvent extraction and stripping phases of copper recovery procedures. Optimizing copper recovery and preserving the effectiveness of the solvent extraction system depends upon controlling the amounts of these components and comprehending how they interact with the extraction process. In this work, the copper bioleaching solution had been treated by solvent extraction using Lix 984N and there had been prior a substantial removal of iron and manganese via oxidation-precipitation using KMnO₄/Ca(OH)_2. Meanwhile, the results of the bioleaching show that the identified bacterial strains by means of 16rRNA sequencing <i>(Leptospirillum ferrooxidans, Acidithiobacillus ferrooxidans, and Acidithiobacillus thiooxidans</i> strains) can successfully bioleach chalcopyrite with a maximum copper extraction of 76.50%. On the other hand, the iron and manganese removal, which consisted of an oxidation in the form of MnO₂ (precipitate), provided a simultaneous manganese and iron removal yield of 95.15 and 98.71%, respectively. The results of solvent extraction show that the copper could be extracted in a single stage at pH = 2.5 with a copper yield of 98.71%, in a 1/1 stochiometric ratio. The raffinate of 50&#xa0;mg/L of Cu was obviously spotted. The stripping can also result in a single stage with 180&#xa0;g/L acidity (H₂SO₄) of the phase.</p> Graphical Abstract <p></p>