The main concern of this study is to develop a feasible and economical technique to microbially recover metals from oxide low-grade ores. Owing to the significant quantities of metals that are embodied in low-grade ores and mining residues, these are potential viable sources of metals. In addition, they potentially endanger the environment, as the metals they contain may be released to the environment in hazardous form. Hence, mining industries are seeking an efficient, economic technique to handle these ores. Pyrometallurgical and hydrometallurgical techniques are either very expensive, energy intensive or have a negative impact on the environment. For these reasons, biohydrometallurgical techniques are coming into perspective. In this study, by employing Aspergillus niger, the feasibility of recovery of metals from a mining residue is shown. A. niger exhibits good potential in generating a variety of organic acids effective for metal solubilization. Organic acid effectiveness was enhanced when sulfuric acid was added to the medium. Different agricultural wastes such as potato peels were tested. In addition, different auxiliary processes were evaluated in order to either elevate the efficiency or reduce costs. Finally, maximum solubilization of 68%, 46% and 34% were achieved for copper, zinc and nickel, respectively. Also iron co-dissolution was minimized as only 7% removal occurred.