Nanoscale materials offer enormous opportunities for catalysis, sensing, energy storage, and so on, along with their superior surface activity and extremely large surface area. Unfortunately, their strong reactivity causes severe degradation and oxidation even under ambient conditions and thereby deteriorates long-term usability. Here superlative stable graphene-encapsulated nanoparticles with a narrow diameter distribution prepared via in situ chemical vapor deposition (CVD) are presented. The judiciously designed CVD protocol generates 3 nm size metal and ceramic nanoparticles intimately encapsulated by few-layer graphene shells. Significantly, graphene-encapsulated Co3O4 nanoparticles exhibit outstanding structural and functional integrity over 2000 cycles of lithiation/delithiation for Li-ion battery anode application, accompanied by 200% reversible volume change of the inner core particles. The insight obtained from this approach offers guidance for utilizing high-capacity electrode materials for Li-ion batteries. Furthermore, this in situ CVD synthesis is compatible with many different metal precursors and postsynthetic treatments, including oxidation, phosphidation, and sulfidation, and thus offers a versatile platform for reliable high-performance catalysis and energy storage/conversion with nanomaterials.