Custom-made proton exchange membranes (PEM) are synthesized by incorporating sulfonated poly(ether ether ketone) (SPEEK) in poly(ether sulfone) (PES) for electricity generation in microbial fuel cells (MFCs). The composite PES/SPEEK membranes at various composition of SPEEK are prepared by the phase inversion method. The membranes are characterized by measuring roughness, proton conductivity, oxygen diffusion, water crossover and electrochemical impedance. The conductivity of hydrophobic PES membrane increases when a small amount (3–5%) of hydrophilic SPEEK is added. The electrochemical impedance spectra shows that the conductivity and capacitance of PES/SPEEK composite membranes during MFC operation are reduced from 6.15 × 10⁻⁷ to 6.93 × 10⁻⁵ (3197 Ω–162 Ω) and from 3.00 × 10⁻⁷ to 1.56 × 10⁻³ F, respectively when 5% of SPEEK added into PES membrane. The PES/SPEEK 5% membrane has the highest performance compared to other membranes with a maximum power density of 170 mW m⁻² at the maximum current density of 340 mA m⁻². However, the interfacial reaction between the membrane and the cathode with Pt catalyst indicates moderate reaction efficiency compared to other membranes. The COD removal efficiency of MFCs with composite membrane PES/SPEEK 5% is nearly 26-fold and 2-fold higher than that of MFCs with Nafion 112 and Nafion 117 membranes respectively. The results suggest that the PES/SPEEK composite membrane is a promising alternative to the costly perfluorosulfonate membranes presently used as separators in MFC systems.