Milk and milk products are an integral part of the human diet and provide benefits to people of all age groups. The authenticity of milk and milk products has become a major concern to scientists, farmers, customers, and policymakers from all over the world. The substitution of part of milk fat or protein with other sources of fats and proteins (e.g., plant) and inter-mixing of milk from different species (cow, buffalo, camel, goat, sheep, etc.) are some of the important practices that are facing criticism all over the world since they compromise the authenticity and nutritional safety of dairy products. To detect these malpractices, a variety of analytical methods based on chromatographic, electrophoretic, and immune-enzymatic approaches were developed. The profiling of metabolites (e.g., low-molecular-weight organic molecules in milk and milk products) is emerging as a new technique for its characterization. The metabolite profile of milk depends on species, breed of animal, conditions, stage of lactation, and diet. Further, during processing and storage of milk and milk products, metabolites are generated due to the action of microorganisms and enzymes present in milk. Therefore, evaluation of these metabolites may help in predicting nutritional properties, technological properties, quality of milk, and bioactivity of milk and also in detecting adulteration in milk. Metabolite profiling of milk can also be used to monitor the health and physiological status of milch animals. The study of metabolites is known as metabolomics, which has provided opportunities to identify the specific markers for nutritional and quality control of milk and milk products, formulate milk and milk products per consumer demand, and also manage livestock by the diagnosis of disease and stress in animals. The identification and quantification of these metabolites of milk and milk products requires high-end analytical techniques such as nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography–mass spectrometry (LC-MS) and gas chromatography–mass spectrometry (GC-MS).