Designing active, selective and stable zeolites for industrial catalytic applications requires insights into deactivation phenomena and their dependence on catalyst and reaction properties. During toluene methylation at high temperatures (573‒773 K), the influences of reaction and transport on the complex reaction network determine reactivity–selectivity–deactivation behavior. At lower temperatures (<433 K), kinetically controlled toluene methylation rates and xylene isomer selectivities are dictated by the (de)stabilization of transition states via van der Waals interactions with voids of varying dimensions. Here, we investigate the deactivation phenomena observed during toluene methylation at low temperatures (403 K) and reactant conversions (<1%). Gas-phase product analysis on varying aluminosilicates (MFI, TON, BEA, FAU, MCM-41) and regeneration studies (853 K) of MFI zeolites in inert gas (He) flow indicate that slower-diffusing C9+ aromatics formed via xylene methylation cascades accumulate within intracrystalline micropores at lower temperatures (403 K), thereby blocking access to active sites. Deactivation rates on MFI samples with fixed active site density increase with increasing crystallite sizes, reflecting the increasing intracrystalline residence times of deactivation precursors and the concomitantly decreasing ratios of internal H+ sites (0.55‒0.70 nm) to external H+ sites (>2.0 nm). A deactivation model, fitted to measured rate data, reveals that deactivation rate constants of internal H+ sites are at least 10× larger than those of external H+ sites. The results of co-feed experiments with external H+ site poisons and the strong dependence of deactivation rate constants on reactant pressures further support the conclusion that deactivation rates reflect the accumulation of bulky polymethylated aromatics within intracrystalline domains, which depends on their relative rates of formation and diffusion within zeolite crystallites. Together, these findings elucidate the deactivation phenomena during low-temperature toluene methylation catalysis in zeolites and further provide insights into catalyst design, reactor operation, and regeneration strategies to mitigate deactivation.