This work proposes an efficient desulfurization system to produce low sulfur diesel under sustainable and moderate experimental conditions. Treatment of a real diesel with a sulfur content of 2300 ppm led to 80% desulfurization after 2 h. The processes used conciliate liquid-liquid extraction and sulfur oxidative catalysis. The catalytic performance of the commercial Keggin-polyoxomolybdate H3[PMo12O40] (PMo12) was strategically increased by simple cation exchange, using a long carbon chain (ODAPMo12, ODA = CH3(CH2)17(CH3)3N), and by its incorporation into the Metal-Organic Framework (MOF) NH2-MIL-101(Cr), forming a new active heterogeneous PMo12@MOF composite catalyst. Activity of both catalysts was similar; however, the solid catalyst could be easily recovered and reused, and its stability was confirmed after multiple continuous cycles.