Addressing the surface chemistry of silicon is of fundamental scientific and technical significance due to the wide use of this material in electronics and optics. A novel method of functionalizing silicon (Si) via short peptides with binding specificity for Si is presented. The peptide presenting the highest affinity for Si is identified via phage display technology, and the 12-mer LLADTTHHRPWT and SPGLSLVSHMQT peptides were found to be specific for the n+-Si and p+-Si surfaces, respectively. In our sensing application, the obtained peptides are used as functionalizing linkers to allow porous silicon microcavities to bind biotin and then capture streptavidin. Molecular detection is monitored via reflectometric interference spectra as shifts in the resonance peaks of the cavity structure. An improved streptavidin sensing (21 times lower detection limit) with peptide-functionalized porous silicon microcavities is demonstrated, compared to sensing performed with devices functionalized with the commonly used silanization method, suggesting that the modification of Si via Si-specific peptides provides better interface layers for molecular detection. High-resolution atomic force microscopy images corroborate this result and reveal the formation of ordered nanometer-sized molecular layers when peptide-route functionalization is performed.