Bifunctional catalysts based on MFI zeolite with 0.5 wt% nickel have been synthesized. The study aimed to evaluate the activity and selectivity of MFI-type zeolites in hydrogen and ammonium forms with nickel nanoparticles in the hydroisomerization and hydrocracking of n-hexane. Samples were investigated using XRD, TEM, and low-temperature nitrogen adsorption/desorption. Nickel was doped into zeolite by both impregnation and ion exchange techniques. Ion exchange was discovered to contribute to the creation of the tiniest metal particles concentrated within zeolite micropores. However, such localization, due to its spatial closeness to the Brönsted acid sites, accelerates the transfer of nickel to the oxidized state, leading to the strengthening of the Brönsted acid sites, and therefore hexane cracking is increasing. As a result, the catalyst target selectivity reduces. It was determined that, regardless of the manner of introduction, Ni-containing (0.5 wt%) catalysts based on HMFI exhibit essentially minimal isomerization activity, but samples based on NH4MFI exhibit a significant increase in isomer yield when 0.5 wt% nickel is added to their composition.