Studies on secondary metabolites such as phenolics have gained enormous popularity due to their potential applications in agriculture, human nutrition, and health. In plants they play a critical role in plant defense and pollination. In humans, plant phenolic compounds are reported to be involved in lowering the oxidation stress diseases due to their anti-inflammatory, anti-allergic, and anti-carcinogenic activities. They are present in different types of plant tissues and foods, but extracting and characterizing them is challenging due to their presence in complex matrices. Plant metabolomics utilizing liquid chromatography (LC) and/or as chromatography (GC) coupled with tandem mass spectrometry (MS) is ideal for identifying and quantitating a wide range of primary and secondary plant metabolites, including phenolics. This chapter discusses the most relevant studies from recent years related to the analysis of polyphenols in various matrices using comprehensive LC–MS/GC-MS.