Zeolite MFI is one of the most important stable porous materials used in catalysis and separation processes. However, some fundamental properties remain in the dark, such as the effect of different aluminum distributions on diffusion. This work, through calculations on cation probability densities, guest energy profiles, and diffusion coefficients, provides a consistent picture of accessibility and mobility for two representative adsorbates, methane and carbon dioxide, and helps to explain the stark differences in diffusion behavior among varying aluminum distributions. A distribution was identified close to the practical limit of maximum aluminum substitution and sodium cation content that actually leads to a collapse in diffusion. For all aluminum distributions studied, the diffusion properties are closely linked to the number of cations. Compensating aluminum negative charge with divalent calcium instead of monovalent sodium increases methane but decreases carbon dioxide diffusion. With respect to increasing adsorbate loading, it induces a monotonous decrease in self-diffusivities for all structures studied. This study highlights the desirability of controlling the aluminum substitution location and, more importantly, the fact that two heavily substituted MFI zeolites with identical composition reported in the literature may have very different diffusion properties.