Fischer–Tropsch synthesis has two main challenges related to direct production of gasoline fuels. First, the chain length distribution of the products follows a broad and unselective Anderson–Schulz–Flory distribution. Second, mostly linear hydrocarbons are formed in the Fischer–Tropsch reaction, thus requiring isomerization while manufacturing gasoline fuels. The present paper addresses a synthetic strategy for the preparation of hierarchical metal and zeolite nanocomposite catalysts for direct synthesis of iso-paraffins from syngas. The nanocomposites are synthesized in three steps. In the first step, the parent (core) zeolite is etched with an ammonium fluoride solution. The etching creates small mesopores inside the zeolite crystals. In the second step, the Ru nanoparticles prepared using water-in-oil microemulsion are deposited in the mesopores of the zeolite. In the third step, a zeolite shell of MFI-type zeolites (silicalite-1 or ZSM-5) is grown on the parent zeolite crystals coating both the etched surface and metallic nanoparticles. Thus, the metal nanoparticles become entirely encapsulated inside the zeolite matrix. Most important parameters such as ruthenium content, zeolite mesoporosity, and more particularly, the acidity of the catalyst shell, which affect the catalytic performance of the synthesized nanocomposite materials in low-temperature Fischer–Tropsch synthesis were identified in this work. The higher relative amount of iso-paraffins was observed on the catalysts containing a shell of ZSM-5. The proximity between metal and acid sites in the zeolite shell of the nanocomposite catalysts is a crucial parameter for the design of efficient metal zeolite bifunctional catalysts for selective synthesis of gasoline-type fuels via Fischer–Tropsch synthesis, while the acidity of the catalyst core has only a limited impact on the catalytic performance.