It is commonly accepted that the digestibility of the proteins of a protein-rich food can be affected by the spatial arrangement of its components, so that two foods with similar macronutrient composition may show different digestibility if produced through different technological processes. Few studies address this topic in vivo, due to the difficulties in setting up a suitable protocol, while a great variety of in vitro digestion tests are described in the literature. Recently the authors of the present paper described one protocol mostly based on Nuclear Magnetic Resonance (NMR) in its Time Domain (TD) and high resolution (HR) variants. TD-NMR measurements at 0.23–0.46 Tesla can be applied to get information about the spatial arrangements of several kinds of food through the interactions between biopolymers and water. Amino acids, peptides and proteins solubilised by digestion can be simultaneously observed by means of HR-NMR, which offers qualitative information about the size distribution of macromolecules by means of the measure of signal linewidth. The present paper focuses on practical aspects of the application of TD- and HR-NMR to the setting up of protocols for the study of the relationships between the structure of protein-rich foods and their digestibility. For this purpose, details on a recently published study describing the protocol set for evaluating the in vitro digestion of Parmigiano cheese by TD- and HR-NMR are given. Some comparisons with other matrices, such as fresh and cured meat, are provided as well.