Thermoplastic starch-based nanocomposites with varying glycerol content and montmorillonite as a nanofiller were studied using dynamic-mechanical analysis (DMA), X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) during one-year storage. DMA results showed that starch-rich and glycerol-rich domains were present in the samples and during storage for up to one year the content of the amorphous phase decreased and molecular mobility changed. 13C NMR and XRD measurements confirmed that ordered structures were formed during storage and its content was larger for samples with higher glycerol content and increased with the storage time. The data obtained from deconvolutions of 1H broad line NMR spectra indicate increased overall molecular mobility in the samples up to four months of storage, while after nine months the trends were opposite. Lower free water content compared to the total water content in the samples determined according to deconvoluted 1H MAS (magic-angle spinning) NMR spectra indicated that a part of water molecules was immobilized in the ordered structures.