In Carbon Molecular Sieve (CMS) membranes, the separation of O2 and N2 is primarily based on the difference in size between the gas molecules. To enhance the separation properties of these CMS membranes it is necessary to functionalize the carbon matrix with materials that show a high affinity to one of the permeating gas species. Adding Ag-nanoclusters increases the selectivity of O2 over N2 by a factor 1.6 compared to a non-functionalized CMS membrane prepared by the same pyrolysis procedure. We have analyzed the structure of Ag-nanocluster (dcluster≈50 nm) containing membranes produced from different Ag sources, AgNO3 and AgAc, and with different Ag content (0, 6, 25, and 40 wt.%). By measuring the pure gas permeabilities of He, CO2, O2, and N2 we have determined the effect of Ag-nanoclusters in the carbon matrix, concluding that in the case of pure gases, the Ag-nanoclusters act primarily as a spacer at pyrolysis end temperatures up to 600 °C, increasing the O2 permeability by a factor of 2.4. However, they enhance the separation of O2 over N2 at higher pyrolysis end temperatures (700 and 800 °C). It was shown that the build up of an Ag layer on the surface of the membrane reduces the permeability, but does not affect the selectivity.