The dynamic behavior of guest molecules that are dissolved in water inside the pores of mesoporous materials is important in many fields of research and applications. We demonstrate the exchange dynamics of methionine and dipeptides of alanine inside the pores of SBA-15 by using ¹H and ²H MAS NMR. These guest molecules may experience intramolecular motion as well as the exchange process. Our results present the rate constants of this exchange process at different hydration levels and sample temperatures, and indicate that these molecules have backbone binding to the silanol sites on the SBA-15 surface similar to alanine (through their N terminus), but show specific intramolecular mobility during the exchange process.