In the current study, a water treatment approach integrating freezing technology, so-called cryopurification, and microbial fuel cell (MFC) process is proposed and tested towards zinc removal. Contaminated water samples used for laboratory experiments were received from the Faro Mine site, Yukon, Canada. Through cryopurification, the effect of freezing temperature, mixing and the direction of ice front propagation on zinc removal from the Faro mine water was investigated and quantitively analyzed. The MFC was used to treat a post-cryopurification brine, both at a laboratory scale. When the coolant temperature ranged from − 5 to − 1 ̊C and 180 rpm solution mixing was used, up to 80–95% of zinc was removed after a single freezing cycle. The results of laboratory experiments demonstrated that zinc concentrations in mine water can be reduced by cryopurification to 0.5 mg/L (effluent quality standard) under optimal experimental conditions. The MFC process was run for 120 h to test the capacity of the microorganism (Shewanella oneidensis) towards zinc removal from the brine concentrated by freezing. Based on the results of laboratory experiments, MFC showed a reliable and high zinc removal up to 90–93% with Shewanella oneidensis incubated in the anode. The MFC generated a power density and open-circuit voltage with a maximum result of 8.8 mW/m2 and 168.5 mV, respectively.