Proton exchange membrane fuel cells (PEMFC) have received a lot of interest and use metal–organic frameworks (MOF)/polymer nanocomposite membranes. Zeolite imidazole framework-90 (ZIF-90) was employed as an addition in the sulfonated poly (1, 4-phenylene ether-ether-sulfone) (SPEES) matrix in order to investigate the proton conductivity in a novel nanocomposite membrane made of SPEES/ ZIF. The high porosity, free surface, and presence of the aldehyde group in the ZIF-90 nanostructure have a substantial impact on enhancing the mechanical, chemical, thermal, and proton conductivity capabilities of the SPEES/ZIF-90 nanocomposite membranes. The results indicate that the utilization of SPEES/ZIF-90 nanocomposite membranes with 3wt% ZIF-90 resulted in enhanced proton conductivity of up to 160 mS/cm at 90 °C and 98% relative humidity (RH). This is a significant improvement compared to the SPEES membrane which exhibited a proton conductivity of 55 mS/cm under the same conditions, indicating a 1.9-fold increase in performance. Furthermore, the SPEES/ZIF-90/3 membrane exhibited a remarkable 79% improvement in maximum power density, achieving a value of 0.52 W/cm2at 0.5 V and 98% RH, which is 79% higher than that of the pristine SPEES membrane.