Nuclear Magnetic Resonance (NMR)-based metabolomic profiling is a powerful analytical technique for characterizing the biochemical composition of functional foods. This chapter explores the fundamental principles of NMR spectroscopy in metabolomics, focusing on its role in identifying metabolites, bioactive compounds, and food authentication by nutritional quality assessment. NMR metabolomics examines essential nutrients, including macro- and micronutrients, and secondary metabolites that influence metabolic pathways, highlighting their relevance in functional food science. The materials required for metabolomic profiling include sample selection protocols, deuterated solvents, buffer solutions, and spectrometer specifications, all of which are followed to ensure precision and accuracy in metabolite extraction and spectral handling, in accordance with GMP standards. Furthermore, the first step of NMR spectroscopy is sample preparation, solvent extraction protocols, and then advanced NMR applications such as 2D spectroscopy and High-Resolution Magic Angle Spinning (HRMAS) NMR. The selection of extraction or NMR methods depends totally on the desired outcomes. In addition, post-processing and statistical-computational strategies enhance the accuracy of metabolite classification. NMR-based metabolomic profiling acts as a transformative tool for functional food studies. It also contributes to personalized nutrition, ensures food safety, and helps to build therapeutic dietary applications.