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Imidazole-doped nanocrystalline cellulose (CNC-Im) is a new proton conductor based on imidazole-functionalized nanocrystalline cellulose with a conductivity of approximately 10⁻¹ S/m at 160 °C. Its conductivity is possible due to the transport of protons from imidazoles. The dynamics of local processes were studied by ¹⁵N and ¹³C nuclear magnetic resonance (NMR) spectroscopy under the conditions of ¹H⁻¹⁵N and ¹H⁻¹³C cross-polarization (CP) and magic angle spinning (MAS) and by heteronuclear correlation (HETCOR) spectroscopy. The ¹⁵N and ¹³C NMR spectra showed the coexistence of two fractions of imidazole molecules: slowly reorienting and exchanging protons and fast reorienting and fast exchanging protons. Analysis based on the two-phase model enabled the determination of the energy distribution of imidazole tautomerization, whose maximum value is 38 kJ/mol. The HETCOR experiment allowed determination of the binding of nitrogen protons from imidazoles to cellulose hydroxyl groups and possibly residual water. NMR studies conducted on the ¹³C isotope confirmed the reorientation of imidazoles. The proton transport in CNC-Im was shown to consist in the exchange of protons between imidazoles via the OH groups of cellulose and residual water conditioned by the reorientation of imidazole rings. The described proton transport leads to the observed conductivity in CNC-Im, assuming the dissociation of imidazole into anion and cation additionally.