Plants are reservoirs of naturally occurring chemical constituents with a wide range of structural diversity. These biological compounds can be derived from different parts of plants such as leaves, barks, seeds, seed coats, flowers, and roots. A broad array of secondary metabolic compounds is present in the plants such as antibiotics, alkaloids, antimicrobials, food-grade pigments, and phenolics which have been reported to possess numerous health-related benefits, including antioxidant, anti-inflammatory, anticancer, and antiobesity activities. Therefore, the identification and detection of these compounds are of utmost importance in order to utilise their benefits into various fields. Wherein, magnetic resonance techniques, such as NMR (nuclear magnetic resonance), MRI (magnetic resonance imaging), and EPR (electron paramagnetic resonance), being far more reproducible, nondestructive, than other analytical techniques such as liquid chromatography, mass spectroscopy, and high-performance liquid chromatography cover a much wider dynamic range of metabolites with easy sample preparation techniques with high speed and fidelity. Hence, these magnetic resonance techniques have been proven to be extremely useful in plant metabolite profiling and disease metabolomics, along with structural elucidation of bioactive compounds from plant sources. Therefore, the present review focuses on the effectiveness of magnetic resonance for the detection of plant-derived metabolites that may lead to new areas of research in various fields such as drug discovery and development, metabolomics, combinatorial chemistry, and assessing overall food safety and quality.