Formation of coke in large H-ZSM-5 and H-SAPO-34 crystals during the methanol-to-olefin (MTO) reaction has been studied in a space- and time-resolved manner. This has been made possible by applying a high-temperature in-situ cell in combination with micro-spectroscopic techniques. The buildup of optically active carbonaceous species allows detection with UV/Vis microscopy, while a confocal fluorescence microscope in an upright configuration visualises the formation of coke molecules and their precursors inside the catalyst grains. In H-ZSM-5, coke is initially formed at the triangular crystal edges, in which straight channel openings reach directly the external crystal surface. At reaction temperatures ranging from 530 to 745 K, two absorption bands at around 415 and 550 nm were detected due to coke or its precursors. Confocal fluorescence microscopy reveals fluorescent carbonaceous species that initially form in the near-surface area and gradually diffuse inwards the crystal in which internal intergrowth boundaries hinder a facile penetration for the more bulky aromatic compounds. In the case of H-SAPO-34 crystals, an absorption band at around 400 nm arises during the reaction. This band grows in intensity with time and then decreases if the reaction is carried out between 530 and 575 K, whereas at higher temperatures its intensity remains steady with time on stream. Formation of the fluorescent species during the course of the reaction is limited to the near-surface region of the H-SAPO-34 crystals, thereby creating diffusion limitations for the coke front moving towards the middle of the crystal during the MTO reaction. The two applied micro-spectroscopic techniques introduced allow us to distinguish between graphite-like coke deposited on the external crystal surface and aromatic species formed inside the zeolite channels. The use of the methods can be extended to a wide variety of catalytic reactions and materials in which carbonaceous deposits are formed.