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.