This paper deals with hydrotreating of straight-run gasoline (SRG) and diesel oil fractions (DOF) over new Ni (Co) containing alumina/zeolite catalysts, modified by transition metals (W and Mo) with the addition of P and Ce elements. In hydrotreating of the DOF, the CoO-WO3-CAR catalyst has the highest hydrodesulphurization activity that reaches 97.2% at 400 °C, P = 4MPa and V = 2h−1. Moreover, increasing of pressure until 5 MPa leads to reducing of the sulfur content up to 0.0007%. The greatest decrease in the pour (−58.9 °C) and the cloud (−56.7 °C) points during the hydrotreating of the DOF is observed using the NiO-MoO3-CAR catalyst. The octane number of SRG after hydrotreating over the NiO-MoO3-CAR catalyst rises up to 88.6. Obtained results clearly show that using synthesized catalysts, motor fuel with Euro-5 standard could be obtained.