Catalyst deactivation during the methanol-to-hydrocarbons (MTH) reaction was investigated using five different commercially prepared microporous catalysts, including Mordenite, ZSM-22, ZSM-5, zeolite Beta and SAPO-34. The reaction was carried out in a fixed bed reactor at a constant feed rate per gram of catalyst. Deactivated and partially deactivated catalysts were obtained at increasing reaction times. The whole of the catalyst beds were characterized using nitrogen adsorption, thermogravimetric analysis, a dissolution-extraction protocol, and UV-Raman spectroscopy, focusing primarily on methods suitable for the quantification of the coke. The results illustrate that topology is the dominant parameter that influences not only catalyst lifetime and product distribution, but also the nature of the species causing the deactivation. For all catalyst topologies, when the entire catalyst bed is examined together, the micropore volume and BET surface area decrease more rapidly than total coke from TGA increases at short reaction times. In the materials with the more restricted access to the internal voids, such as ZSM-22 and SAPO-34, the loss of activity is to a large extent due to species which are soluble in dichloromethane and give rise to distinct features in the Raman spectra. For the Mordenite and Beta catalysts, which have larger pores comprising three dimensional networks, and to some extent for the ZSM-5 catalyst employed, the accumulation of more coke species which are insoluble in dichloromethane, presumably on the external surface of the zeolite crystals, is observed. This is linked to the appearance of more pronounced D and G bands in the Raman spectra, indicative of extended carbon species.