Nafion based proton exchange membrane (PEM) has long been used as conventional PEM in direct methanol fuel cell (DMFC) industry. However, the high cost of Nafion membrane and other drawbacks like high methanol crossover hinder the advancement of this industry. This study aims to develop a low cost membrane using sulfonated poly ether ether ketone (SPEEK) polymer. Silica and silicotungstic acid (SiWA) were incorporated into the membrane matrix using solution casting method. The optimum loading of the additives was tuned and it is discovered that the SPEEK membrane containing 10 wt% of silica and 5 wt% of SiWA has the best performance due to its high proton conductivity and moderately low methanol permeability. The performance of the membrane can further be enhanced by adding (3-aminopropyl)triethoxysilane (APTES) and carbonyldiimidazole (CDI) as coupling agents. Inclusion of APTES and CDI in SPEEK could not only improve the compatibility between organic SPEEK and inorganic additives, but also improve the homogeneity and dispersity of the additives. As a result, the resultant membrane with a better dimensional stability achieves high selectivity (10.60 × 104 S.s/cm3) up to 6.5 times more than pristine SPEEK membrane and 1.3 times higher than the commercial Nafion 117 membrane. •SPEEK/SiO2-SiWA was produced with APTES as coupling agent and CDI as promoter.•SPEEK1-AC achieved selectivity of 6.5 times higher than pristine SPEEK.•Silica-supported SiWA increased the proton conductivity of SPEEK membrane.•Improvement in homogeneity between organic SPEEK and inorganic additives.