A novel strategy to sequentially recover and separate Sn(II), Fe(II) and Cu(II) from a synthetic wastewater from printed circuit board (PrCB) manufacturing in a single microbial fuel cell (MFCSn)‐MFCFe‐MFCCu process was achieved, where in‐situ produced caustic was primarily utilized for Sn precipitation (MFCSn) and then secondly used for Fe deposition (MFCFe) and anaerobic Cu(II) reduction in the final MFCCu. An external resistance of 1000 Ω in the MFCSn and MFCFe, and a 10 Ω resistor in the MFCCu achieved predominant recovery of Sn (MFCSn: 80.8±0.8 %), Fe (MFCFe: 59.1±0.8 %), and Cu (MFCCu: 68.2±1.8 %) in the three MFCs, with separation factors of 32.1±1.6 for Sn (MFCSn) and 7.5±1.8 for Fe (MFCFe), and complete recovery of Cu (MFCCu, 42‐mesh cathodes). The metal concentrations in the final effluent were below national discharge limits (Sn, 2.0 mg/L; Fe, 5.0 mg/L; Cu, 0.2 mg/L). The metal recoveries ranged from 2.6 (Sn, MFCSn)–12.0 (Cu, MFCCu), and the separation factors were 8.4 (Sn, MFCSn)–∞ (Cu, MFCCu) times those of the open circuit controls. Cathodes with 120‐mesh size of stainless steel mesh produced lower metal recoveries [33.7 % (Sn, MFCSn) and 27.0 % (Fe, MFCFe) decrease] and separation factors than MFCs with 42‐mesh cathodes. This study provides a viable approach for efficiently recovering and separating Sn, Fe and Cu from stripping solutions produced in PrCB manufacturing, with simultaneous power production.