We studied the isomerization mechanism of 1-cycle-hexyloctane either in gas phase or inside zeolites using quantum models. In the gas phase the reaction was simulated following the classical scheme via carbocations. On the other hand, the isomerization reaction was modeled with 1-cycle-hexyloctane inside HZSM-22 and H-Y acid zeolites (condensed phase). We used the ONIOM(B3LYP/6-31G: UFF) hybrid method to study such behavior in both zeolites. Our results show that the reaction follows different pathways when the simulations are performed either in gas phase or within the zeolites pores. Such differences show the importance of quantum confinement inside microporous materials.