The permeation characteristics of palladium pore filled (PF) membranes have been investigated with gas permeation and structural characterization of the membranes. PF membranes have been prepared by filling with Pd the nanoporous γ-Al2O3/YSZ (or pure YSZ) layer supported onto porous α-Al2O3 and ZrO2. The number of nanoporous layers and the applied vacuum level during the electroless plating process have been studied. Gas permeation properties of the PF membranes have been determined in a temperature range of 300–550 °C. The measured hydrogen permeances have been found to be lower than previously reported for similar membranes. It has been found that the hydrogen fluxes do not depend on the thickness of the nanoporous layers (γ-Al2O3/YSZ or pure YSZ) or on the vacuum pump employed for filling with Pd. The physicochemical characterization performed showed that the palladium deposited does not form a percolated network across the mesoporous layer(s), leading to low hydrogen permeances and thus low H2/N2 perm-selectivities.