Mesoporous silica-based materials (SBA-15, TUD-1, HMM-33, KIT-6, FSM-16, etc.) with spongy-like structure are high-efficient candidates for the manufacture of ion exchange membranes (IEMs). According to the literatures, the more functionalized sites, the higher ions transfer can be achieved. In the present work, we chose KIT-6 functionalized with sulfonic groups to embed into the sulfonated poly ether sulfone (SPES) as the composite membrane and have evaluated its performance in a microbial fuel cell (MFC). Structural analysis of membranes demonstrated that S-KIT-6 with percentage of 1.5 could create a smooth surface with acceptable hydrophilicity which not only improved proton exchange  ability, but also increase power production of the system. The characterization results were in agreement with experimental data. The MFC working with SPES/S-KIT-6-1.5% could achieve the highest power density with value of 0.824±0.02 Wm2 which was 8-fold and 35.82-fold higher than that of Nafion 117 and SPES, respectively. S-KIT-6-1.5% could recover 57.8% of the generated electrons whereas; maximum COD removal belonged to SPES/S-KIT-6-0.7% with the amount of 94.5±6.2%. We introduced the new mesoporous materials modified membranes that have high potential to be installed in the MFCs and meet their needs.