Abstract Nickel and molybdenum nanoparticles were prepared on silicon aluminum phosphate (SAPO-11) and mesoporous silica (SBA-15), respectively, and compared with γ-Al2O3 support. Results showed that the nickel and molybdenum nanoparticles were located inside the pores of the SBA-15 structure with particles sizes around 7 nm. However, for the SAPO-11 support the nanoparticles are dispersed outside the support surface. These catalysts were tested for hydrodeoxygenation (HDO) and exhibited excellent catalytic activity. The catalytic reaction had been carried out in a fixed bed flow reactor at 200–300 °C. It is noteworthy that the Turnover Frequencies (TOF) obtained for of NiMoSAPO was 2 times greater than NiMoSBA-15 catalyst. The products formed on NiMoSAPO and NiMoSBA were completely different from the NiMoAl2O3 catalyst used as reference. IR of Pyridine suggested that the hydrodeoxygenation and hydrodearomatization reaction is strongly affected by the support nature, specifically, due to the relation between Bronsted and Lewis acid sites present at the surface of these materials. The low surface area, dispersion of the metallic sites and the proportion of Lewis/Bronsted acid sites have had strong influence on the selectivity of the hydrodeoxygenation reaction.