To investigate the impact of the surface functionalization of mesoporous silica nanoparticle (MSN) carriers in the physical state, molecular mobility and the release of Fenofibrate (FNB) MSNs with ordered cylindrical pores were prepared. The surface of the MSNs was modified with either (3-aminopropyl) triethoxysilane (APTES) or trimethoxy(phenyl)silane (TMPS), and the density of the grafted functional groups was quantified via1H-NMR. The incorporation in the ~3 nm pores of the MSNs promoted FNB amorphization, as evidenced via FTIR, DSC and dielectric analysis, showing no tendency to undergo recrystallization in opposition to the neat drug. Moreover, the onset of the glass transition was slightly shifted to lower temperatures when the drug was loaded in unmodified MSNs, and MSNs modified with APTES composite, while it increased in the case of TMPS-modified MSNs. Dielectric studies have confirmed these changes and allowed researchers to disclose the broad glass transition in multiple relaxations associated with different FNB populations. Moreover, DRS showed relaxation processes in dehydrated composites associated with surface-anchored FNB molecules whose mobility showed a correlation with the observed drug release profiles.