The plant-based diet has been encouraged over the years, as it has been strongly associated with a reduction of several chronic degenerative diseases. This beneficial effect of plant-based foods and their co-products on human health may be related to their high levels and diversity of polyphenols, secondary metabolites that act in defense against external pathogens during plant growth, whereby several epidemiological studies point to their great bioactive effect. Over the years, different techniques have been applied with the aim of mapping the profile and phenolic content in various plant matrices; however, metabolomics stands out as a sensitive and reliable tool. Although it shows advantages over other analytical techniques, metabolomics requires several steps, from sample preparation to data analysis, which vary according to the sample and the final goal sought when performing the analysis. Thus, this chapter presents the detailed steps of metabolomic analysis in plant-based foods, medicinal plants, and agro-industrial residues, highlighting current studies where this tool was efficiently applied along with future perspectives.