A two-stage hybrid Constructed Wetland (CW) integrated with a microbial fuel cell (MFC), and microbial electrolysis cell (MEC) has been assessed for treatment performance and clogging assessment and further compared with CW. The CW-MEC was operated with applied potential to the working electrode and compared with the performance of naturally adapted redox potential of the CW-MFC system. A complex synthetic municipal wastewater was used during the study, which was composed of trace metals, organics, inorganics, and dye. The study demonstrated that providing a constant potential to the working electrode in CW-MEC has resulted in high treatment performance and reduced sludge generation. The maximum chemical oxygen demand (COD), ammonium (NH4+), and phosphate (PO43-) removal achieved during treatment by CW-MEC at 24 h hydraulic retention time was 89 ± 6%, 72 ± 6% and 93 ± 2%, respectively. ICP-MS results indicated that trace metal removals were also higher in CW-MEC than in CW alone (p < 0.05). At the end of the experiment, significant volumetric change (total volume of the microcosm) occurred in CW (1.3 L), which indicates high sludge generation, whereas it was lesser in CW-MEC (0.3 L) and in CW-MFC (0.5 L). Further, Energy Dispersive X-ray (EDX) spectroscopy results indicated low levels of metal precipitation in the CW-MEC system. Based on the Shannon diversity index, the CW-MEC was assessed to be characterised by high species richness and diversity. The observations from this study indicate that the applied potential at the working electrode has a significant impact on treatment performance and clogging behaviour of the system.