Properties of ion exchange membranes (IEMs) both cationic and anionic were widely analysed before and after chemical. The modification aims to reduce the crossover phenomena typically observed in RFBs by incorporating polypyrrole (PPy) at the inner of commercial IEMs. In this work, we have explored the insight of membranes by structural and generalized conductivity considerations and its implications in terms of physicochemical characteristics. Transport Structural Parameters (TSP) have been obtained from the electrolyte concentration dependencies (NaCl, in this work). AEMs successfully increased their specific conductivity (between 2.5 and 3.9 times) whereas CEMs slightly decreased (between 1.3 and 2 times). This approach was useful for the description of membrane electro-transport by using the so-called two-phase model which considers an IEM as an heterophase system (particularly, gel and interstitial phase) and their arrangement. AEMs almost doubled increased whereas CEMs doubled decreased their internal microphase arrangement in terms of structural parameter (α). A modification of the established model was applied to the CEMs to better understand their specific behaviour after polymerization. Up to 3.5 times the diffusion coefficient was obtained in AEMs after PPy modification. Finally, based on TSP obtained we propose a microstructural description for the IEMs studied in this work.