Here, a novel, versatile synthetic strategy to fabricate a yolk–shell structured material that can encapsulate virtually any functional noble metal or metal oxide nanocatalysts of any morphology in a free suspension fashion is reported. This strategy also enables encapsulation of more than one type of nanoparticle inside a single shell, including paramagnetic iron oxide used for magnetic separation. The mesoporous organosilica shell provides efficient mass transfer of small target molecules, while serving as a size exclusion barrier for larger interfering molecules. Major structural and functional advantages of this material design are demonstrated by performing three proof-of-concept applications. First, effective encapsulation of plasmonic gold nanospheres for localized photothermal heating and heat-driven reaction inside the shell is shown. Second, hydrogenation catalysis is demonstrated under spatial confinement driven by palladium nanocubes. Finally, the surface-enhanced Raman spectroscopic detection of model pollutant by gold nanorods is presented for highly sensitive environmental sensing with size exclusion.