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Herein, we report sol-gel modified sulfonated poly(ether ether ketone) (SPEEK) organo-silane based composite proton exchange membranes for their suitability in direct methanol fuel cells (DMFCs). Different concentrations (0.2–1.5 wt%) of aminopropyl trimethoxysilane (APTES) are incorporated in SPEEK matrix by in-situ sol-gel method. Physico and electrochemical performances of composite membranes are enhanced by induced H-bonding interactions between free –NH 2 and –SO 3 H groups. With increase in APTES concentration to 0.8 wt%, the ionic conductivity illustrates improvement by ⁓80% while IEC and Proton conductivity (Pc) enhances by ∼21% and ∼70%, respectively than SPEEK. To further explore the feasibility of the membranes in DMFC. Methanol crossover resistance is calculated to as low as 5.30 × 10−7 cm2 s−1 and offers highest selectivity of 4.43 S s cm−3 in contrast to 12.55 × 10−7 cm2 s−1 and 0.31 S s cm−3 for SPEEK, respectively. This study reveals that the Si-SPEEK membrane is a potential alternate for DMFC. • SPEEK matrix is loaded with APTES to enhance membrane properties. • Organosilicon-based acid-base stable membranes are prepared. • 0.8 wt% APTES showed overall improved physiochemical and electrochemical properties. • H-bonding interaction improved thermal and mechanical stability. • Alternate cation exchange membrane for DMFC is prepared. [ABSTRACT FROM AUTHOR]