Regulations on the permissible levels of sulfur in transportation fuels are becoming ever more strict, with a global shift towards “zero sulfur” fuels, and the revamp of existing hydrodesulfurization (HDS) facilities to meet these lower caps is cost‐prohibitive. Metal‐catalyzed sulfoxidation chemistry is viewed as an economically viable desulfurization strategy that could complement conventional HDS technology. In the present work, the complex [η5‐IndMo(CO)3Me] (1) (Ind = indenyl) was employed in the catalytic oxidative desulfurization (CODS) of model and real liquid fuels, using aqueous hydrogen peroxide (H2O2) as oxidant. After optimization of the CODS reaction parameters (diesel/H2O2 ratio, catalyst amount, temperature), a high‐sulfur (2000 ppm) model diesel containing benzothiophene, dibenzothiophene, 4‐methyldibenzothiophene and 4,6‐dimethyldibenzothiophene could be completely desulfurized within 2 hr under solvent‐free conditions or in the presence of the ionic liquid 1‐butyl‐3‐methylimidazolium hexafluorophosphate ([BMIM]PF6) as extraction solvent. The catalyst formed under solvent‐free conditions could be recycled without a significant decrease in desulfurization activity. The high performance of the CODS system was verified in the sulfur removal from a commercial untreated diesel fuel with a sulfur content of 2300 ppm, and a jet fuel with a sulfur content of 1100 ppm. Solvent‐free CODS in combination with initial/final extraction gave desulfurization efficiencies of 70% for the diesel fuel and 55% for the jet fuel. CODS with [BMIM]PF6 in combination with initial/final extraction led to a sulfur removal of 95.9% for the diesel fuel, which is one of the best results yet reported for ODS of commercial diesels.