Mesoporous silica materials have been studied for the time-dependent delivery of bioactive agents. It has already been shown that ibuprofen molecules can be encapsulated with loading as high as 30 wt% in MCM-41 silica, functionalized or not by amino groups. Interactions between the guest molecules and the host matrix have been investigated by 1H, 29Si and 13C solid state NMR spectroscopy. These experiments demonstrate an extremely high mobility of the ibuprofen molecules when the matrix is not functionalized, despite of the presence of a carboxylic function on the ibuprofen molecules. On the contrary, when the silica matrix is functionalized by amino groups, the 13C NMR response shows a strong restriction in mobility suggesting the existence of interactions between the amino groups and the carboxylic groups.