m-Xylene isomerisation, as well as secondary disproportionation reactions, were examined over the 10-ring zeolites with different pore topology. As recognised in Py-sorption IR studies, all the 3D zeolites tested, i.e. IM-5, TNU-9, and ZSM-5 delivered the same protonic functionality, both in the manner of the amount and strength of the Si(OH)Al groups. Only zeolite TNU-10 provided lower number of Brønsted acid sites due to the limited accessibility of the sites hidden in the 8-ring system. Two-dimensional correlation spectroscopy (2D COS) analysis was applied to investigate the dataset obtained from IR spectroscopic studies. Both diffusion characteristics, as well as the different size of internal cavities, were found as crucial parameters determining the catalytic effectiveness. The presence of intermediate species, whose the origin is related to the distortion of the substrate molecule geometry during the adsorption process was recognised for all the studied structures. Such species are believed to be represented by the 1485 cm−1 band and assigned to the intermediate arenium ions, e.g. methylbenzenium ions, CH3–C6H5+–CH3. Both m-xylene and intermediate were consumed for coke precursors in the most spacious zeolite TNU-9. The production of p-xylene was detected only in the first period of the reaction, then coke formation was proved to be the privileged process. The simultaneous loss of m-xylene and methylbenzenium ions was also detected for the zeolite IM-5. Both species underwent isomerisation to p-xylene. No formation of coke species was observed for less spacious structures, i.e. ZSM-5 and TNU-10. The generation of isomerization products was found to be the most rapid in TNU-10. The formation of the intermediate species correlates with other products in the first minutes of the reaction (1–6 min), then the consumption to other reaction products distort the correlation.