This work reports the alterations in the performance and morphology of a Nafion-based proton exchange membrane in the presence of three nano-Co3O4 morphologies (nanorod (R), nanosphere (S), and nanooctahedral (O)) modified by tetraethylorthosilicate (TEOS, T) and 3-aminopropyltriethoxysilane (APTES, A). The effects of surface chemistry and morphology of Co3O4 nanostructures on the properties of the as-prepared nanocomposite membranes were investigated by water uptake, proton conductivity, methanol permeability, and selectivity measurements. The methanol barrier properties of all nanocomposite membranes improved compared to the control Nafion membrane. The Nafion membranes embedded with aminosilica-functionalized Co3O4 also showed higher proton conductivity and improved methanol barrier properties compared to silica-functionalized Co3O4 and unmodified nanoparticles owing to the strong interaction between amino functionals on the surface of Co3O4 nanostructures and sulfonic moieties of the Nafion matrix. In particular, the incorporation of 5 wt % octahedral aminosilica-functionalized Co3O4 into the Nafion matrix provided the highest selectivity (15.2 × 104 S s–1 cm–3) and the lowermost methanol permeability (5 × 10–7 cm2 s–1), which were 3.6-fold higher and four times lower than that of the control Nafion membrane, respectively.