Phosphonated graphene oxide (pGO) has been incorporated to sulfonated poly(styrene-isobutylene-styrene) (SO3H SIBS) to prepare polymer nanocomposite membranes (PNMs) for direct methanol fuel cell (DMFC) and chemical and biological protective clothing (CBPC) applications. The performance of the membranes was evaluated per SIBS sulfonation level (i.e. 38, 61, and 90 mole %), filler type (i.e. GO and pGO) and filler loading (i.e. 0.1, 0.5 and 1.0 wt.%). The transport properties (i.e. proton conductivity and methanol and vapor permeability) were determined to assess the performance of the PNMs per each application. The ionic interactions between the phosphonic and sulfonic groups (i.e. PO3H2 and SO3H, respectively) altered the pathways of SO3H SIBS, influencing the transport of permeants through the membranes. SIBS 61 pGO 0.1 presented the highest separation efficiency and a DMFC performance comparable to the state-of-the-art Nafion®, indicating that this membrane could potentially be implemented as protective fabric as well as functioning for fuel cell applications.