Mixed matrix membranes (MMMs) based on NH2-functionalized MIL-53(Al) and MIL-101(Al) MOFs dispersed in polysulfone (PSF) and polyimide (PI) polymers have been investigated. The MOF loading was varied in the range of 8–25 wt.%, while membranes with different thicknesses were obtained by two casting methodologies. The synthesized membranes were tested in the separation of CO2 from an equimolar CO2/CH4 mixture. At steady operation (T = 35 °C, ΔP = 3 bar), incorporation of the MOF filler has a positive effect on the separation performance which consists of a moderate enhancement of the separation selectivity, in certain cases along with an improvement in CO2 permeability. In general, higher separation factors and CO2 permeabilities are achieved with PI than with PSF. Our study reveals the relevance of the membrane thickness for both the separation performance under given conditions and the sensitivity to other structural and operational variables. The incorporation of NH2-MIL-53(Al) as filler in PI-based MMMs has a larger effect, particularly a beneficial increment in CO2 permeability at constant separation factor, for thinner membranes casted in a Doctor Blade system. This is tentatively attributed to the partial preservation of the original narrow pore configuration of this flexible MOF, unlike in thicker membranes casted in the absence of shear forces. Although improvements in the separation performance remain moderate with respect to the neat PI counterpart, the benefits of the incorporation of MOF as filler become more apparent at high pressures: while for pure polymeric membranes a decrease in the separation factor is observed at increasing ΔP, MMMs maintain large separation factors up to transmembrane pressures as high as 12 bar, highlighting the application potential of these composites. On the other hand, reducing the membrane thickness limits the MOF loading that can be incorporated before the mechanical stability of the membrane becomes compromised. It also enlarges the impact of the temperature and trans-membrane pressure on the separation performance. Overall, this work reveals that an interplay between structural and operational variables determines the performance of MOF MMMs and calls for a multi-variable optimization to advance this technology.