Three-dimensional-intracrystalline diffusion structures were prepared from a 1D/12MR-HZSM-12 zeolite that was desilicated with NaOH solutions at different temperatures. The results showed that carefully tuned desilication preserved most of the crystalline structure and revealed that even though the strong acid sites had decreased, the hierarchical zeolites exhibited similar initial activities compared to that of the 1D-microporous precursor. Moreover, the new textural and acid properties of the desilicated zeolites strongly improved the catalytic stability during cyclohexane conversion. That stability, a key factor to be considered in the engineering scale-up of the catalyst, resulted from the decrease of the strong acid sites and more importantly from improvements in the molecular diffusion inside of the new 3D-intracrystalline porous structure that decreased the contact time, minimizing subsequent reactions that could lead to coke formation, thus avoiding deactivation. Otherwise, the presence of mesopores favored the selectivity to C6 cyclohexane isomers.