The infiltration of enhanced green fluorescent protein (EGFP) into nanochannels of different diameters in mesoporous silica particles was studied in detail by fluorescence microspectroscopy at room temperature. Silica particles from the MCM-41, ASNCs and SBA-15 families possessing nanometer-sized (3–8 nm in diameter) channels, comparable to the dimensions of the infiltrated guest protein EGFP (barrel structure with dimensions of 2.4 nm × 4.2 nm), were used as hosts. We found that it is necessary to first functionalize the surfaces of the silica particles with an amino-silane for effective encapsulation of EGFP. We demonstrated successful infiltration of the protein into the nanochannels based on fluorescence microspectroscopy and loading capacity calculations, even for nanochannel diameters approaching the protein dimensions. We studied the spatial distributions of the EGFPs within the silica particles by confocal laser scanning microscopy (CLSM) and multimode microscopy. Upon infiltration, the fluorescence lifetime drops as expected for an emitter embedded in a high refractive index medium. Further, the spectral properties of EGFP are preserved, confirming the structural integrity of the infiltrated protein. This inorganic-protein host–guest system is an example of a nanobiophotonic hybrid system that may lead to composite materials with novel optical properties.