Metal zeolite composite catalysts have found numerous applications in adsorption, gas separation, petroleum refining and chemical industry. The key issue in the design of these catalysts is the localization of the metal within the zeolite structure. This paper focuses on a new approach to the synthesis of nickel-zeolite composite catalysts selectively containing metal nanoparticles inside the zeolite pores. In the catalysts prepared by conventional impregnation, metal particles from the external surface of the zeolites were selectively removed by extraction with bulky polymer molecules of poly-4-styrenesulfonic acid. The method is particularly suitable for the ZSM-5 zeolite with relatively narrow micropores. The nickel zeolite catalysts were tested in hydrogenation of toluene and 1,3,5 – tri-isopropyl benzene (TIPB). The removal of nickel particles from the zeolite external surface leads to a considerable decrease in the hydrogenation rate of the bulky TIPB molecules, while toluene hydrogenation was affected to a much lesser extent and was almost proportional to the nickel content. The proposed methodology can be extended to other types of microporous catalysts.