A successful encapsulation of Keggin-type polyoxomolybdate (H[PMoO], PMo) into metal-organic framework (MOF) materials with an identical framework but distinct metal centers (ZIF-8 with Zn and ZIF-67 with Co) was accomplished by a straightforward room-temperature procedure. The presence of Zn in the composite material PMo@ZIF-8 instead of Co in PMo@ZIF-67 caused a remarkable increase in the catalytic activity that achieved a total oxidative desulfurization of a multicomponent model diesel under moderate and friendly conditions (oxidant: HO and solvent: ionic liquid, IL). Interestingly, the parent ZIF-8-based composite with the Keggin-type polyoxotungstate (H[PWO], PW), PW@ZIF-8, did not show the relevant catalytic activity. The ZIF-type supports present an appropriate framework to accommodate active polyoxometalates (POMs) into their cavities without leaching, but the nature of the metallic center from the POM and the metal present in the ZIF framework were vital for the catalytic performance of the composite materials.