Oligonucleotide solid-phase synthesis is now possible on nano-sized particles, thanks to the use of controlled pore glass-nanoparticle assemblies. We succeeded in anchoring silica nanoparticles (NPs) inside the pores of micrometric glass via a reversible covalent binding. The pore diameter must be at least six times the diameter of the nanoparticle in order to maintain efficient synthesis of oligonucleotides in the synthesizer. We demonstrated that the pores protect NP anchoring during DNA synthesis without decreasing the coupling rate of the phosphoramidite synthons. This bottom-up strategy for NP functionalization with DNA results in unprecedented DNA loading efficiency. We also confirmed that the DNA synthesized on the nanoparticle surface was accessible for hybridization with its complementary DNA strand.