Polydimethylsiloxane (PDMS) is one of the most widely used materials for the fabrication of microfluidic devices. The uncomplicated integration of ion-exchange membranes, such as Nafion (R), would facilitate manifold electrochemical processes in microfluidics. However, the Nafion ionomer does not directly bond with crosslinked PDMS and the assembly of the membrane and PDMS substrate still remains a technological challenge. This work reports a straightforward procedure using a simple bifunctional silane as crosslinking agent to directly integrate Nafion membranes into PDMS structures. The procedure applies a plasma treatment for both Nafion membrane and PDMS substrate to generate reactive surface functional groups that covalently bond with the functional groups of the silane, resulting in the formation of a strong chemical bonding across the interface. Peel tests prove the robust and uniform bonding that is also stable in acidic solutions. The ion conductivity of the bonded Nafion is comparable to that of the commercial Nafion.