This work focuses on quantification of microscopic self-diffusion of gas molecules in mixed-matrix membranes (MMMs) formed by dispersing UiO-66-NH2 metal–organic framework (MOF) crystals in 6FDA-Durene polyimide. Self-diffusion measurements were performed by 13C pulsed field gradient nuclear magnetic resonance (PFG NMR) for pure CO2 and CH4 with the spatial resolution in the range of 0.5–24 μm and for different MOF loadings between 12.5 and 50 weight percent. Diffusion measurements performed for each gas in the MMM with the lowest MOF loading of 12.5 weight percent yielded a single diffusivity for all measured diffusion times corresponding to a diffusion under the condition of a fast exchange between the UiO-66-NH2 crystals and the surrounding polymer phase. However, as the UiO-66-NH2 loading was increased, two molecular ensembles were observed for both CO2 and CH4: 1) an ensemble corresponding to diffusion inside UiO-66-NH2 crystals and through the MOF–polymer interfaces, and 2) an ensemble corresponding to diffusion mainly in the polymer phase of the MMMs. This behavior can be explained by the formation of MOF clusters at higher MOF loadings. Quantification of the intra-cluster diffusivity, average cluster size, and the dependence of these properties on the MOF loading are presented and discussed. The reported measurements can serve as a framework to quantify discrete microscopic diffusion characteristics and sizes of interconnected MOF clusters in MMMs as MOF loading increases to reach the desired outcome of gas percolation over a spanning MOF cluster, viz a cluster of interconnected MOF crystals spanning an entire MMM.