The fundamental mechanisms of biologically active molecule adsorption and release from ordered mesoporous silica are discussed in terms of the variation of surface electrochemistry after functionalization. Specifically, ordered mesoporous SBA-15 has been grafted with aminopropyl, etilenediamine, phosphatoethyl, propyl methacrylate, and carboxylic acid groups at different degrees of functionalization. To test the molecular adsorption and release features, three molecules of clinical interest have been selected, namely, antiresorptive zoledronic acid, amino acid L-tryptophan, and protein bovine serum albumin. Molecular loading and delivery aspects have been studied by emphasizing the host-guest interactions, which determine the adsorption and release behavior. It has been found that careful control of surface electrochemistry by functionalization determines the bioactive molecule adsorption whereas the release can be mainly thought of as a diffusion matter dependent on the surface area and molecule size. This enhanced approach opens up new ways to optimize molecule loading for specific clinical needs.