The present work deals with the treatment of bio digester effluent (BDE) using electrocoagulation (EC) followed by continuous membrane less microbial fuel cell (CML‐MFC). BDE with high organic load and low biodegradability index (BI) is first treated with EC process, which removes organic load and improves the BI of treated BDE. Further the EC treated BDE with relatively low organic load 1000 mg/L and considerable BI (~0.42) is used as a substrate solution for the CML‐MFC process. It is noted that the BDE with initial organic load of 2500 mg/L can be successfully treated using only EC process, whereas, only CML‐MFC operation can successfully teat EC treated BDE with low organic load (1000 mg/L). However, in combined study of EC followed by CML‐MFC, the BDE with initial organic load of 7450 mg/L can be successfully treated to achieve effluent composition below permissible limit as per Central Pollution Control Board (CPCB) norm. It is also computed that under the experimental conditions, during the EC process, approximately 2.466 and 0.537 kJ/g of energy can be generated from sludge and scum, respectively, whereas, approximately 48 mV voltage and 0.02 mA current can be generated from the CML‐MFC process. © 2019 American Institute of Chemical Engineers Environ Prog, 38:e13139, 2019