Redox probe transport through supported lipid bilayers and nanopore‐confined lipid assemblies on silica thin films is examined using electrochemical impedance spectroscopy (EIS). These supported lipid systems are emerging biomimetic separation and sensor platforms. The ability to quantify the accessibility of the pore structure of the mesoporous silica thin films is demonstrated, which is essential for the incorporation of carriers into the lipids for selective solute transport. Redox probe molecules with varying hydrophilicity are used to compare ion transport in supported lipid pore‐spanning bilayers (enveloped bilayers) and novel lipid filled pores of mesoporous silica thin films. The films feature orthogonally oriented 8–10 nm cylindrical nanopores formed by deposition of P123‐templated silica sols onto chemically modified fluorine‐doped tin oxide. Nanopore accessibility is confirmed by EIS with hydrophilic probe 1,1′‐ferrocenedimethanol (FDM). Filling the pores with lipid 1,2‐dipalmitoyl‐sn‐glycero‐3‐phosphocholine results in a superior barrier (with roughly 1/9 the permeability) to transport of FDM compared to fragile enveloped lipid bilayers deposited by vesicle fusion. The pore‐confined lipids not only provide a better barrier to FDM, but also a better pathway for the transport across the films of a hydrophobic redox probe 1,1′‐dioctadecyl‐4,4′‐bipyridinium dibromide, with an ideal transport selectivity of 11 compared to FDM.