In the microbial fuel cells (MFCs) driven capacitive deionization (CDI) process, the electricity generated from MFCs can be utilized for downstream deionization processes in the CDI cell. However, due to the typical configuration of MFCs, i.e., anaerobic anode and aerobic cathode compartments, the MFC effluent still contains various ionic pollutants, e.g., NO3- and PO43-. In this study, we present the proof-of-concept of an integrated MFC-CDI process for advanced wastewater treatment: the cost-effective continuous-flow MFCs perform as secondary treatment for organic carbon and ammonium removal, electricity production; the energy-efficient CDI cell works as the tertiary treatment to enhance the purification and desalination of domestic wastewater effluent. The results indicated that approximately 90% of the chemical oxygen demand (COD) and ammonium were removed in the MFCs. CDI, powered by connecting two MFCs in parallel and associated with a potential of 0.49 V, could subsequently remove multi-ionic species from the MFC-treated effluent. More specifically, nutrient ions (NO3- and PO43-) can be electrostatically removed by the CDI process. These results demonstrated that the integrated MFC-CDI technology, which harvested energy from wastewater, held great potential to be an advanced, energy-saving purification process for the simultaneous removal of carbonaceous pollutants, improved nutrient removal, and further electrosorptive desalination of domestic wastewater treatment, in order to achieve a sustainable water-energy system. They also showed that, in addition to effluent quality improvement, the tertiary electrosorption of CDI played a significant role in the stability of effluent quality so as to dampen variations in the quality of secondary-treated effluent.