An efficient procedure for aerobic oxidation of thiols to disulfides catalyzed by new self-assembled hierarchical mesoporous Mn–MFI in the presence of air under solvent-free conditions as well as in aqueous medium is reported. The mesoporosity and Mn4+ loading, together with a highly crystalline microporous pore wall structure of the MFI framework were achieved through a newly designed hydrothermal process. This hydrothermal approach leads to hierarchical self-assembled mesoporous zeolite structures through isomorphous substitution of Si by Mn and Al. It is shown that Mn-containing mesoporous zeolites are capable to form disulfide bonds from thiols in the presence of air. The zeolitic materials were characterized by XRD, field-emission scanning electron microscopy, high-resolution TEM, X-ray photoelectron spectroscopy, 29Si NMR, 27Al NMR, and EPR spectroscopy, as well as AAS analysis and N2 sorption studies. N2 sorption analysis revealed high surface areas and narrow pore size distributions (1.2–6.0 nm) for different samples. The mesoporous Mn–ZSM-5 acted as an efficient heterogeneous catalyst with maximum catalytic activity in the benzenethiol conversion to diphenyldithiol.