Chiral alkyl aryl sulfoxides were obtained by molybdenum-catalyzed oxidation of alkyl aryl sulfides with hydrogen peroxide as oxidant in mild conditions with high yields and moderate enantioselectivities. The asymmetry is generated by the use of imidazolium-based dicarboxylic compounds, HLR. The in-situ-generated catalyst, a mixture of aqueous [Mo(O)(O2)2(H2O)n] with HLR as chirality inductors, in the presence of [PPh4]Br, was identified as the anionic binuclear complex [PPh4]{[Mo(O)(O2)2(H2O)]2(μ-LR)}, according to spectroscopic data and Density Functional Theory (DFT) calculations. A nonclassical hydrogen bond between one C–H bond of the alkyl R group of coordinated (LR)− and one oxygen atom of the peroxido ligand was identified as the interaction responsible for the asymmetry in the process. Additionally, the step that governs the enantioselectivity was theoretically analyzed by locating the transition states of the oxido-transfer to PhMeS of model complexes [Mo(O)(O2)2(H2O)(κ1-O-LR)]− (R = H, iPr). The ∆∆G≠ is ca. 0 kcal∙mol−1 for R = H, racemic sulfoxide, meanwhile for chiral species the ∆∆G≠ of ca. 2 kcal∙mol−1 favors the formation of (R)-sulfoxide.