The morphology in terms of the ion channel size, apparent porosity and tortuosity of perfluorosulfonated membranes was modified by using sulfonated polystyrene (SPS) as a sacrificial porogen. The precursor polymers were fabricated via solution-casting of the commercially available Nafion solution together with SPS. Upon swelling SPS was leached from the membrane matrix resulting in the formation of larger nanosized ion channels and clusters and hence a more open membrane matrix in fully hydrated conditions. Below a threshold value of 30% SPS, the membranes maintained high permselectivity and the porogen mainly increased the apparent porosity and network interconnectivity resulting in increased hydraulic permeability, streaming potential coefficient and membrane conductivity. Higher porogen contents resulted in larger characteristic hydrophilic domain sizes, quantified from SAXS/WAXS, and enhanced membrane conductivity up to 300% with only a slight decrease in the permselectivity in dilute LiCl solutions. These results together confirm the effective modification of the charged nanoscopic ion network and clearly indicate that SPS can efficiently be used for precise tuning the PTFE-based membrane matrix to achieve tailored transport properties for specific electrochemical applications.