High levels of sulfur organic compounds (SOCs) and nitrogen organic compounds (NOCs), which are contaminants present in diesel fuel and straight run gas oil (SRGO), were removed using tungsten/zirconia catalysts and hydrogen peroxide by oxidative desulfurization and oxidative denitrogenation reactions. Two tungsten sources were used: tungstic acid and ammonium metatungstate. The catalysts obtained by anionic exchange at low pH with tungstic acid showed remarkable homogeneity and high W dispersion attributed to tetrahedral W species and full dibenzothiophene (DBT) oxidation was achieved in 5 min of reaction. On the other hand, the catalysts obtained by impregnation with ammonium metatungstate developed mainly octahedral species with less DBT oxidation. It was also found that tetrahedral species generate more acidity than octahedral species. A density functional theory computational study confirmed the observed DBT oxidation trend shown by tetrahedral and octahedral W species on the peroxide-activated catalysts. Diesel fuel and SRGO were desulfurized and denitrogenated to a high extent: 97% in diesel fuel and 70% in SRGO for sulfur compounds and 96% in diesel fuel and 89% in SRGO for nitrogen compounds, whereas C-1-C-3 dibenzothiophenes, 4-methyl dibenzothiophene, and 4,6-dimethyl dibenzothiophene were fully removed. The elimination of SOCs and NOCs present in fuels can be effectively carried out in a single process to obtain clean fuels.