Citrus fruits have been cultivated since ancient times and are highly popular worldwide. Global citrus fruit production reached 15.849 million tons in 2020; about a third of these fruits are consumed as processed juice, canned, marmalade, jelly, and dehydrated products, of which juice is the most popular. Citrus juice is a significant source of water, nutrients, and phytochemicals. Metabolomics is a new technology used for examining small-molecule (<1500 Da) metabolites that have been extensively applied for comparing, evaluating, assessing the authenticity, and annotating the novel markers in citrus juice. A Web of Science search using the keywords “fruit juice metabolomics” yielded 229 publications, 69 of which concerned “citrus juice metabolomics.” This chapter highlights the metabolomics workflow while providing an updated, comprehensive overview of the most useful metabolomics-based techniques and the widely used applications for citrus juice metabolomic data interpretation. It is expected to improve the methodologies for juice analysis and provide insight into the raw fruit selection, processing, quality control, and nutritional evaluation of citrus juice.