Surface functionalization methods were investigated for their effects on the sensing performances of porous silicon (p-Si) microcavities when used for detection of biomolecules. These microcavities were fabricated to reveal reflectivity pass-band spectra in the visible and near-infrared spectral regime. In one approach, the devices were thermally oxidized and functionalized to ensure covalent binding of molecules. In the second approach, the as-etched p-Si surface was modified with adhesion peptides, isolated via phage display, that present high binding capacity for silicon. Functionalization and molecular binding events were monitored via reflectometric interference spectra as shifts in the resonance peaks of the cavity structure due to changes in the refractive index when a biomolecule is attached to the large internal surface of p-Si. Improved sensitivity was obtained owing to the peptide interface linkers between the p-Si and biological molecules compared to the silanized devices. Investigating the formation of peptide–Si interface layer via X-ray photoelectron spectroscopy, scanning tunneling microscopy, and scanning electron microscopy, we found that peptides form nanometer-thin layers on the Si surface and that their binding energy depends on the sequence of the peptide.