Alkene skeletal isomerization elementary steps catalyzed by acid zeolites are key reactions in refining, petrochemistry and biomass conversion. We unravel the atomic-scale origin of the higher rate constant of type A isomerization (involving a direct alkyl transfer, without any change in the branching degree) than the one of type B isomerization (involving non-classical carbonium ions such as protonated cyclopropane (PCP), inducing a change in the branching degree) of C-7 carbenium ions in chabazite. Accurate free energy barriers are calculated at 300 and 500 K for both reactions by means of molecular dynamics in combination with blue moon ensemble approach, whereas the static approach is shown to fail to describe these reactions. The slow transformation between individual rotational isomers, causing nonergodic sampling of reactant state, largely overlooked in literature, is carefully addressed in the present work. At 500 K (representative of experimental conditions), free energy barriers of 83.4 kJ/mol and 15.0 kJ/mol are determined for type B and type A isomerization respectively. The much lower barrier for type A is thus recovered, and assigned to a loose transition state, with free rotation of the migrating alkyl group, while the transition state of type B isomerization is tighter, with such a rotation blocked, due to the simultaneous hydride shift taking place on the edge of the PCP. (C) 2019 Elsevier Inc. All rights reserved.