Plant metabolomics is a set of fast-moving, analytical and chemometric tools and methods for plant functional genomics, phenotyping and systems biology. This multidisciplinary “omics” science can deliver qualitative and quantitative data that provide a detailed description of biochemical systems that are influenced by environmental changes, such as plant–pathogen interactions. This chapter examines key insights and recent outputs in the field of phytopathological metabolomics with a specific focus on the perturbations of primary compounds involved in central metabolism and infection-related metabolites including phytohormones. Priming of plant immune responses is also considered through the angle of metabolomics. Furthermore, the chapter highlights the recurring challenges in the distinction of host and pathogen metabolomes and the hurdles of metabolome annotation. The chapter concludes with perspectives indicating key avenues in ongoing efforts to decode metabolic landscapes of plants under biotic stress conditions.