Zeolite catalysts exhibit microporous structures, akin to the pockets in naturally occurring enzyme catalysts, which enable the confinement of reaction intermediates, thus facilitating chemical transformations. Nonetheless, the micropores also influence the formation of coke species, which is the main source of catalytic activity loss. Unveiling the relationships between the micropore topology and the internal structure and location of deactivating coke compounds is of high relevance for comprehending the deactivation mechanisms. In this study, we used an approach exploiting powder neutron diffraction to assess the location of coke and determine the dominating structures in the topologically distinct ZSM-5 (MFI topology), ZSM-35 (FER), and SSZ-13 (CHA) zeolite catalysts deactivated in industrially relevant methanol-to-hydrocarbon (MTH) conversion. In ZSM-5 and ZSM-35 catalysts, coke resides along the straight 10-membered ring (MR) channels and exhibits the highest concentration in their intersecting regions with sinusoidal 10 MR and straight 8 MR pores, respectively. In the SSZ-13 catalyst, coke is not only located in cages but also protrudes through their 8 MR windows, suggesting the interconnectivity of coke molecules between the large cavities. Notably, the coke-associated signals in the ZSM-5 and ZSM-35 catalysts show a strong planar arrangement that can be fitted by polycyclic and monocyclic arene structures, respectively. These averaged coke structures are consistent with the composition of coke assessed by gas chromatography–mass spectrometry, 13C and two-dimensional 1H double-quantum single-quantum magic-angle spinning nuclear magnetic resonance, and operando diffuse reflectance ultraviolet–visible spectroscopic analysis. The findings evidence that the pore topology directs the confinement and structure of coke, wherein the largest void zones of the micropore space are the most susceptible to coking.