Membrane-based processes are taking a more and more prominent position in the search for sustainable and energy-efficient gas separation applications. It is known that the separation performance of pure polymers may significantly be improved by the dispersion of suitable filler materials in the polymer matrix, to produce so-called mixed matrix membranes. In the present work, four different organic cages were dispersed in the poly(ether ether ketone) with cardo group, PEEK-WC. The m-xylyl imine and furanyl imine-based fillers yielded mechanically robust and selective films after silicone coating. Instead, poor dispersion of p-xylyl imine and diphenyl imine cages did not allow the formation of selective films. The H2, He, O2, N2, CH4, and CO2 pure gas permeability of the neat polymer and the MMMs were measured, and the effect of filler was compared with the maximum limits expected for infinitely permeable and impermeable fillers, according to the Maxwell model. Time lag measurements allowed the calculation of the diffusion coefficient and demonstrated that 20 wt % of furanyl imine cage strongly increased the diffusion coefficient of the bulkier gases and decreased the diffusion selectivity, whereas the m-xylyl imine cage slightly increased the diffusion coefficient and improved the size-selectivity. The performance and properties of the membranes were discussed in relation to their composition and morphology.