The development of innovative proton-conducting membranes exhibiting an improved [H+/VO2+] ion selectivity in comparison with baseline perfluorinated ionomers (e.g., Nafion) is critical to prompt the large-scale implementation of vanadium redox flow batteries (VRFBs) characterized by a performance and cyclability compatible with the applications. This paper pursues this objective by reporting the preparation and characterization of a new family of hybrid inorganic-organic membranes, that are labeled “[SPEEK/(WO 3 ) x ]”, consisting of a sulfonated poly (ether ether ketone) (SPEEK) matrix hosting between 0 and 23.6 wt% of WO3 nanoparticles (NPs). The physicochemical characterization of the [SPEEK/(WO3)x] membranes elucidates the impact of the introduction of WO3 NPs on the thermal, structural and transport properties of the SPEEK host. It is found that the [SPEEK/(WO3)0.20] membrane presents the highest [H+/VO2+] ion selectivity (2.1 × 104 S min cm−3), that is more than three times higher than that of recast Nafion (6.5 × 103 S min cm−3). [SPEEK/(WO3)0.20] is then mounted in a single cell VRFB, that is tested extensively under realistic operating conditions and demonstrates a coulombic efficiency and cyclabilty that are improved with respect to the corresponding figures of a VRFB incorporating a Nafion 212 membrane to provide the basis for a comparison. This outcome is in compliance with the result of the “ex-situ” investigations, and allows for the proposal of a structural model correlating the physicochemical properties of the [SPEEK/(WO3)x] membranes with the transport properties and the proton conductivity.