Nuclear magnetic resonance (NMR)-based metabolomics has emerged as a robust and reproducible analytical platform for investigating the molecular mechanisms underlying disease and identifying candidate biomarkers with potential clinical relevance. Although initially developed for biomedical research, its application in veterinary medicine has expanded rapidly during the last decade, driven by the growing demand for precision medicine approaches capable of improving disease diagnosis, prognosis and therapeutic monitoring. This review summarizes the current landscape of NMR metabolomics in veterinary medicine, highlighting its applications across major clinical areas, including oncology, infectious, respiratory, digestive, renal, endocrine and musculoskeletal diseases. Collectively, the available evidence demonstrates that NMR metabolomics consistently identifies disease-associated metabolic alterations, providing novel insights into pathophysiology while supporting biomarker discovery in naturally occurring animal diseases. Beyond current clinical applications, we discuss the major challenges that continue to limit routine implementation, including biological variability, standardization of analytical workflows, multicentre validation and clinical translation. Particular attention is given to recent technological advances, such as benchtop NMR instrumentation, artificial intelligence-assisted data analysis, multi-omics integration and the development of collaborative networks and standardized platforms. Together, these advances position NMR metabolomics as a promising technology to support precision veterinary medicine, facilitating its transition from biomarker discovery to routine clinical implementation.