Integrating nanostructured silicon materials with aqueous biological systems requires I suitable chemical passivation that call be controlled in a reproducible fashion. Herein, we investigate in detail a facile method to control both the stability of a porous silicon rugate filter and the degree to which the material can be functionalized with biological molecules. Hydrosilylation of neat and dilute undecenoic acid over time leads to monolayers with different chemical surface coverage within the mesoporous architecture. We show how the shrift in the reflectance spectrum, as a result of the change in the average refractive index of the rugate filter, can be used to assess the coverage of organic molecules oil the pore surfaces. Surfaces with low monolayer coverage dissolve rapidly when exposed to aqueous solutions but are amenable to a high degree of biological functionalization. Surfaces with high coverage show exceptional stability but are biologically modified to a lesser degree. Therefore, tailoring the reaction conditions can be used to suit the application where control of stability and degree of biological modification are important criterion. Surfaces fabricated within the intermediate regime display both good stability and efficient biomolecule conjugation thus making them ideal for sensing applications. Biosensing utility is demonstrated by detecting active protease within the crystal by cleavage of immobilized peptides.