Detailed insight into molecular diffusion in zeolite frameworks is crucial for the analysis of the factors governing their catalytic performance in methanol-to-hydrocarbons (MTH) reactions. In this work, we present a molecular dynamics study of the diffusion of methanol in all-silica and acidic zeolite MFI and Beta frameworks over the range of temperatures 373–473 K. Owing to the difference in pore dimensions, methanol diffusion is more hindered in H-MFI, with diffusion coefficients that do not exceed 10 × 10−10 m2s−1. In comparison, H-Beta shows diffusivities that are one to two orders of magnitude larger. Consequently, the activation energy of translational diffusion can reach 16 kJ·mol−1 in H-MFI, depending on the molecular loading, against a value for H-Beta that remains between 6 and 8 kJ·mol−1. The analysis of the radial distribution functions and the residence time at the Brønsted acid sites shows a greater probability for methylation of the framework in the MFI structure compared to zeolite Beta, with the latter displaying a higher prevalence for methanol clustering. These results contribute to the understanding of the differences in catalytic performance of zeolites with varying micropore dimensions in MTH reactions.