Protein digestion inside the nanoreactor channels of mesoporous silica (SBA-15) is reported, and evaluated by using peptide-mass mapping. Both proteases and substrates were efficiently captured within these biocompatible nanoreactors. After 10 minutes, the mass spectrum of the protein digests released from the mesoporous-silica-based nanoreactors revealed the presence of eight peptides covering 58% of the protein sequence with an intense signal (signal/noise ratio > 70). In comparison, the conventional overnight in-solution digestion of proteins under otherwise identical conditions generated only three peptides (27% sequence coverage). We propose that this order-of-magnitude increase in the proteolytic reaction rate is mainly attributed to two factors: substrate enrichment within mesoporous silica channels and enzyme immobilization. The surface properties and macrostructure of the mesoporous silica were studied to reveal their significant influence on proteolytic reactions.