Biotrophic plant-microbe interactions depend on the establishment of a nutritional interface allowing nutrient trafficking between plants and microbial symbionts and pathogens. A global re-programming of host and microbial metabolism is at the core of these interactions, and we summarise in this chapter studies on metabolome and, to add interpretational power, transcriptome changes associated with the establishment and maintenance of a range of plant?microbe associations. Pathogenic fungi of crops cause severe economic losses, and factors resulting in improved crop resistance against infection and disease spread are therefore the subject of extensive research projects. We focus in this chapter on three fungal examples, namely Magnaporthe grisea (rice blast), Blumeria graminis (powdery mildew) and Ustilago maydis (corn smut), and discuss how metabolomics technologies critically improve our understanding of resistant and susceptible interactions. Like pathogens, mutualistic symbionts are heterotrophic organisms and depend on nutrients from their hosts, but unlike pathogens these microbial symbionts rarely cause disease symptoms or host death. In contrast, they can improve plant fitness by providing valuable nutrients or protective metabolites to their hosts, and we present here insights from studies on three exemplar mutualistic interactions, namely nitrogen fixing legume-rhizobial, phosphorus supplying plant root ? arbuscular mycorrhizal and alkaloid-producing plant shoot ? Neotyphodium spp. endophyte associations. We conclude this chapter with an analysis of similarities and differences of pathogenic and mutualistic interactions from a global metabolic viewpoint, and propose that improved spatial and temporal separation, as well as high-throughput analytical techniques for low abundance metabolites (e.g. phytohormones), might overcome some current limitations.