Dehydration of alcohols into alkenes is a key reaction for the production of fuels and chemicals from biomass. However, the mechanism of these reactions is highly questionable, hindering the rational optimization of efficient catalysts. In the present work, the formation of linear butenes starting from isobutanol catalyzed by proton-exchanged zeolites is unraveled by ab initio molecular dynamics (AIMD). Comparison with static calculations done for a gas phase reaction catalyzed by a proton and for the prototypical chabazite zeolite framework shows that AIMD estimations of the free energy barriers are significantly different from the static ones. Moreover, a common transition state (TS) is found for two competing reactions, namely, the isomerization of isobutanol into butan-2-ol (the dehydration of the latter yielding linear butenes) and the synchronous dehydration and isomerization of isobutanol into products related to linear butenes in a single step. The existence of a post-TS bifurcation prevents a traditional estimation of rates by transition state theory. To circumvent this problem, we quantify relative transmission coefficients using the Bennett–Chandler theory, which shows a clear tendency for decrease of relative frequency for isobutanol isomerization and increase of that for synchronous dehydration and isomerization when switching from 100 to 500 K. This work represents a step forward for the accurate determination of rates for key reactions in alcohol dehydration reactions.