The methanol-to-olefins (MTO) process using methanol from renewable feedstocks has attracted attention as an alternative industrial process to fuels and chemicals. MTO is characterized by a hydrocarbon pool mechanism within the pores of a zeolite consisting of multiple catalytic cycles. In this work, we have investigated the origin of olefins over zeolites ZSM-5 and SSZ-13 using transient operando DRIFTS/GC in which the feed composition is alternated between series of pulses of CH₃OH and CD₃OD. A deuterium isotope effect affects the product distribution and perturbs the catalytic cycles at work to different extents. We could clearly differentiate the pathways leading to the formation of ethene on the one hand and C₃₊ hydrocarbons on the other hand over ZSM-5 at different reaction stages, i.e., during the initial formation of the hydrocarbon pool and after the prolonged exposure to reaction conditions. This differentiation was absent at the beginning of the reaction on SSZ-13, where most of the olefins up to C₄ had a common origin and C₅ olefins started to be produced only after long exposure. By correlating the vibrational shift of the polymethylbenzenium ion identified within the pores of the zeolites and the chromatographic shifts of the products upon deuterium exchange under reaction conditions, we associated the production of ethene in ZSM-5 and most of the C₂–C₄ olefins in SSZ-13 to an aromatic catalytic cycle that has the carbenium ion as a precursor. C₃₊ hydrocarbons over ZSM-5 and C₅ olefins initially over SSZ-13 are instead associated with a different mechanistic origin, which can be reconciled with an olefin catalytic cycle.