Ceramic membranes are widely used in microbial fuel cells (MFCs) owing to their cost-effectiveness and availability. However, these membranes often face challenges such as biofouling and negative mass-transfer effects. This study explored the use of a polymer layer to mitigate these issues, focusing on a polyvinylidene fluoride (PVDF) nanofibre membrane with various surface modifications. The modifications included alkaline treatment (PVDF-OH), rhamnolipids treatment (PVDF/BS), and a combination of both (PVDF-OH/BS). The ceramic membrane integrated with PVDF-OH/BS achieved the highest power density of 13.8 W m−3, which was 38 % higher than that of the unmodified ceramic membrane. Additionally, during the long-term study (days 90–101), the Ceramic + PVDF-OH/BS maintained a 64 % higher power performance compared to the unmodified ceramic membrane, indicating superior antifouling properties. Electrochemical and surface characterisation revealed that rhamnolipid-modified PVDF nanofibers enhanced fouling resistance. The findings demonstrate that natural biosurfactants which can be produced in situ within MFCs, can form a protective layer over membranes and significantly enhance their long-term power performance. This study represents the first instance of using natural microbial biosurfactants to improve membrane efficiency in a bioelectrochemical system.