This contribution describes the preparation of multifunctional yolk–shell nanoparticles (YSNs) consisting of a core of silica spheres and an outer shell based on periodic mesoporous organosilica (PMO) with perpendicularly aligned mesoporous channels. The new yolk–shell hybrid materials were synthesised through a dual mesophase and vesicle soft templating method. The mesostructure of the shell, the dimension of the hollow space (4∼52 nm), and the shell thickness (16∼34 nm) could be adjusted by precise tuning of the synthesis parameters, as evidenced by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and nitrogen sorption investigations. Various metal nanoparticles (e.g., Au, Pt, and Pd) were encapsulated and confined in the void space between the core and the shell using impregnation and reduction of adequate metal precursors. The selective oxidation of various alcohol substrates was then carried out to illustrate the benefits of such an architecture in catalysis. High conversion (∼100%) and excellent selectivity (∼99%) were obtained over Pd nanoparticles encapsulated in the hybrid PMO yolk–shell structures.