The properties of ordered mesoporous silicas as bioactive materials, able to induce bone-tissue regeneration, have been combined with their abilities to host and release specific biomolecules in a controlled fashion. The possibility of locally deliver peptides and proteins is of great scientific importance because it opens new paths for the design of implantable biomaterials than can promote bone formation where needed. These biomaterials can host such biofactors, and their adsorption can be enhanced by chemically modifying the silica surface, with the aim of encouraging host-guest interaction and, thereby, increasing the loading capacity of the biomaterial matrix. L-Tryptophan (L-Trp) is a hydrophobic amino acid present in the three-dimensional structure of numerous proteins, and it is used here as model system to predict peptide delivery systems. Unmodified, silanol-rich, bioactive SBA-15 ordered mesoporous silica has been found to be incapable of confining L-Trp in its mesopores due to the hydrophobic character of this molecule. Organically modifying SBA-15 with quaternary amines results in approximately two-thirds of the silica surface being functionalized, increases the surface hydrophobicity allowing an increased L-Trp loading, and also induces different release kinetics. The control of the L-Trp release is the first step in controlled and localized protein delivery technologies, and opens novel perspectives for designing bioactive silica-based devices suitable for bone-healing applications.