This paper describes a study of the nature of metal-free protonated fibrous silica BEA (HSi@BEA) and its ability to generate protonic acid sites originating from molecular hydrogen and from C-6 alkanes and cycloalkanes. HSi@BEA was successfully synthesized by a microemulsion system and subsequently applied in n-hexane, cyclohexane and methylcyclopentane isomerization. The HSi@BEA consisted of microspheres with a bicontinuous concentric lamellar structure morphology. Its core was mainly composed of an aluminosilicate framework of BEA, while the lamellar structure consisted of silica. The particle size of HSi@BEA was in the range of 400 nm to 700 nm with pore diameters between 3.6 nm to 5.6 nm and 15 nm to 25 nm. Al-27 MAS NMR results showed that the additional silica lamellar structure of the HSi@BEA increased the extra-framework aluminum (AlOH) which acts as Lewis acidic sites in the catalyst. FTIR results revealed that these additional Lewis acid sites in the metal-free catalyst generated a high amount of protonic acid sites by playing a role as electron acceptors after the dissociation of H-2 and C-6 alkane and cycloalkanes. Significantly, the participation of more protonic acid sites enhanced the catalytic performance of the C-6 alkanes and cycloalkanes, n-hexane, cyclohexane and methylcyclopentane, at a low reaction temperature of 423 K. The presence of a silica lamellar structure resulted in a two to threefold higher isomer yield of n-hexane, cyclohexane and methylcyclopentane compared to bare HBEA catalyst which mainly produces cracking products. In addition, a kinetics study showed that the activation energy could be lowered by two to three times at elevated temperatures in the range of 423 K to 623 K.