Protected Designation of Origin cheeses are products with high-quality standards that can claim higher prices on the market. For this reason, non-PDO cheeses with lower quality can be mislabeled as PDO or mixed with it for economic gain especially when the product is in a shredded form. Luckily, the production of PDO cheese is subjected to strict procedural specification rules that result in a product with a defined profile of its metabolites, which can be used for authentication purposes. In this study, an NMR metabolomic approach combined with multivariate analysis was implemented to build a classification model able to discriminate PDO Grana Padano cheese from a large dataset of competitors. The great advantage of the proposed approach is a simple sample preparation, obtaining a holistic overview of the analyzed samples. The untargeted approach highlighted a "typical profile" of Grana Padano samples, which could be used for protection purposes. In parallel, the targeted results allowed us to identify potential chemicals, such as lactate, some amino acids and lipids. These initial results could open the road to a potential new additional tool to check the authenticity of PDO cheeses in the future.