Biogas is a sustainable, renewable energy source generated from organic waste degradation during anaerobic digestion (AD). AD is applied for treating different types of wastewater, mostly containing high organic load. However, AD practice is still limited due to the low quality of the produced biogas. Upgrading biogas to natural gas quality (>90% CH4) is essential for broad applications. Here, an innovative bio-electrochemically assisted AD process was developed, combining wastewater treatment and biogas upgrading. This process was based on a microbial electrolysis cell (MEC) that produced hydrogen from wastewater at a relatively high efficiency, followed by high-rate anaerobic systems for completing biodegradation of organic matter and an in situ bio-methanation process. Results showed that CH4 production yield was substantially improved upon coupling of the MEC with the AD system. Interestingly, CH4 production yield increase was most notable once circulation between AD and MEC was applied, while current density was not markedly affected by the circulation rates. The microbial community analysis confirmed that the MEC enhanced hydrogen production, leading to the enrichment of hydrogenotrophic methanogens. Thus, directing soluble hydrogen from the MEC to AD is plausible, and has great potential for biogas upgrading, avoiding the need for direct hydrogen harvesting.