UDCaT-6, a novel active mesoporous and stable catalyst, was synthesized by generating in situ nanosized acidic centers of chlorosulfonic acid treated zirconia in the pores of highly ordered hexagonal mesoporous silica (HMS). For the first time, we have used chlorosulfonic acid as a source of sulfating agent to treat zirconia in pores of the HMS. The catalyst is characterized by XRD, FTIR, EDAX, SEM, and BET surface area and pore size analysis, and probe reactions. The structural integrity of HMS is maintained in UDCaT-6. The activity and stability of UDCaT-6 was tested in liquid phase alkylation of toluene with benzyl chloride and vapor phase synthesis of tent-amyl methyl ether (TAME) from test-amyl alcohol (TAA) and methanol where corrosive acid HCl and water are generated as biproducts. A complete theoretical and experimental analysis is presented and kinetics are evaluated. The model explains the experimental data very well.