The metabolic profiling of probiotic low-sodium Prato cheeses with addition of food enhancers (arginine, yeast extract, and oregano extract) along the ripening time (1, 30, 60 days) using NMR spectroscopy and chemometric tools (PCA and PLS-DA) was evaluated. Aromatic and aliphatic structures and lactic acid were the most dominant compounds regardless of the flavour enhancer added. The addition of flavour enhancers decreased the lactic acid content and increased the content of leucine, isoleucine, and valine, fatty acids, tyrosine, phenylalanine, histidine, benzoic acid, and formic acid. Principal components analysis differentiated cheese samples based on the contents of lactic, acetic, formic, benzoic, and fatty acids, valine, leucine, isoleucine, tyrosine, phenylalanine, and histidine. Partial least square discriminant analysis classified the cheese types based on composition and highlighted the compounds variability according to the ripening time. NMR spectroscopy and chemometrics may be an effective approach to investigate the metabolic profiling of probiotic cheeses.