The influence of viral infection on crop productivity or yield and quality has been widely studied by various researchers, but their effects on phytochemical profiles, more precisely metabolite biosynthesis, have been underexplored. Plant metabolomics is the subject of studying the phytomolecules present in the plant body, their enzymatic biosynthesis pathways, and classification of the molecules based on that, which helps to identify biomarkers associated with infections, nutrient deficiencies, and other diseases. Therefore, metabolomics can be an effective tool to understand plant-virus interactions. This chapter delivers the role of plant metabolomics and insights into alterations in metabolite profiles of tropical vegetables due to viral infection, which largely affect the yield and biochemical quality of the produce. It focuses on the changes in the biosynthesis pathways of compounds like alkaloids, phenolics, terpenoids, etc. and the role of different plant enzymes in these alterations. Contemporary chromatographic and spectroscopic tools such as GC-MS, LC-MS, HPLC, NMR, etc. have facilitated in-depth investigations on the effects of viruses on phytochemical profiles. Studies on vegetables like okra, tomato, chili, and cucurbits indicate that viral infections can alter metabolic pathways either by upregulating or by downregulating certain metabolite biosynthesis. Some specific metabolites showed increased or decreased levels, where the higher ones were associated with plant defense mechanisms and antimicrobial characteristics, serving as indicators of host-pathogenic interaction. By isolating these biomarker metabolites, we can reveal the chemical alterations of the host plant due to viral infections. It evidently establishes how hosts counter viruses and how the viral pathogens can modify host metabolisms to facilitate infection, rendering plants vulnerable to insect vectors. Therefore, a metabolomics study can aid in our comprehension of the processes underlying infection and viral transmission.