Bacterial nanocellulose (BC)-based composites containing poly(2-hydroxyethyl methacrylate) (PHEMA), poly(methacroylcholine chloride) (PMACC) or poly(methacroylcholine hydroxide) (PMACH) were characterized by inelastic neutron scattering (INS) spectroscopy, combined with DFT (density functional theory) calculations of model systems. A reasonable match between calculated and experimental spectral lines and their intensities was used to support the vibrational assignment of the observed bands and to validate the possible structures. The differences between the spectra of the nanocomposites and the pure precursors indicate that interactions between the components are stronger for the ionic poly(methacrylate) derivatives than for the neutral counterpart. Displaced anions interact differently with cellulose chains, due to the different ability to compete with the O–H···O hydrogen bonds in cellulose. Hence, the INS is an adequate technique to delve deeper into the structure and dynamics of nanocellulose-based composites, confirming that they are true nanocomposite materials instead of simple mixtures of totally independent domains.