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In this research, Zn, Ni, and Cu recovery from mobile phone printed circuit boards was investigated. The initial pH and pulp density using Aspergillus niger or Penicillium simplicissimum fungi were optimized to improve the recovery of Zn, Ni, and Cu using a central composite design. Fungi were able to recover 97% of Cu. Often for Ni recovery, A. niger was more effective, but in low pulp densities and low pH, P. simplicissimum was preferred. For recovery of Zn, A. niger is more appropriate at pH lower than 6, but P. simplicissimum outperforms at pH higher than 6. Under the optimum conditions (pulp density of 4 gL −1 and initial pH 10), the respective recovery of Cu, Ni, and Zn was determined as 94%, 100%, and 100% using A. niger as well as 100%, 95%, and 87% using P. simplicissimum. At alkaline conditions, oxalic acid, citric acid, and gluconic acid are the main acids produced by A. niger; the main acid produced by P. simplicissimum is oxalic acid. Similarly, FTIR and chemical characteristics of the metabolites (the organic acid produced) were analyzed under optimal conditions using HPLC. A. niger in alkaline and acidic conditions produces more acids which lead to higher recovery.