‘Tonda Gentile Romana’ and ‘Tonda di Giffoni’ (Corylus avellanaL.) are two Italian hazelnut cultivars, recognized under the quality labels “Protected Designation of Origin” (PDO) and “Protected Geographical Indication” (PGI), respectively. Hazelnut seeds are characterized by a complex microstructure and the presence of different physical compartments. This peculiarity has been studied and evidenced by Time Domain (TD) Nuclear Magnetic Resonance (NMR) experiments. This technique allowed the assessment of the presence of different diffusion compartments, or domains, by evaluating the distribution of the spin–spin relaxation time (T2).The aim of this research was to develop a method based on1H NMR relaxometry to study the mobility in fresh hazelnut seeds (‘Tonda di Giffoni’ and ‘Tonda Gentile Romana’), in order to determine differences in seed structure and matrix mobility between the two cultivars. TD-NMR measurements were performed from 8 to 55 °C in order to mimic post-harvest processing as well the microscopic textural properties of hazelnut. The Carr–Purcell–Meiboom–Gill (CPMG) experiments showed five components for ‘Tonda Gentile Romana’ and four components for ‘Tonda di Giffoni’ relaxation times. The two slowest components of relaxation (T2,aabout 30–40% of the NMR signal, and T2,babout 50% of the NMR signal) were attributed to the protons of the lipid molecules organized in the organelles (oleosomes), both for the ‘Tonda Gentile Romana’ and for the ‘Tonda di Giffoni’ samples. The component of relaxation T2,cwas assigned to cytoplasmic water molecules, and showed a T2value dominated by diffusive exchange with a reduced value compared to that of pure water at the same temperature. This can be attributed to the water molecules affected by the relaxation effect of the cell walls. The experiments carried out as a function of temperature showed, for ‘Tonda Gentile Romana’, an unexpected trend between 30 and 45 °C, indicating a phase transition in its oil component. This study provides information that could be used to strengthen the specifications underlying the definitions of “Protected Designation of Origin” (PDO) and “Protected Geographical Indication” (PGI).