The rational design of ultra-small metal clusters dispersed on a solid is of crucial importance in modern nanotechnology and catalysis. In this contribution, the concept of catalyst fabrication with a very ultra-small size of platinum nanoparticles supported on a hierarchical zeolite surface via a one-pot hydrothermal system was demonstrated. Combining the zeolite gel with ethylenediaminetetraacetic acid (EDTA) as a ligand precursor during the crystallization process, it allows significant improvement of the metal dispersion on a zeolite support. To illustrate the beneficial effect of ultra-small metal nanoparticles on a hierarchical zeolite surface as a bifunctional catalyst, a very high catalytic performance of almost 100% of cycloalkane product yield can be achieved in the consecutive mild hydrodeoxygenation of 4-propylphenol, which is a lignin-derived model molecule. This instance opens up perspectives to improve the efficiency of a catalyst for the sustainable conversion of biomass-derived compounds to fuels.