Plant metabolomics is a rapidly developing field in the area of biological sciences that has the potential to understand various aspects of plant-microbe interaction. Metabolomics involves extensive investigations of metabolites occurring in the tissues and cells of plants. In natural environments, the plants closely interact with microbes through plant’s roots, shoots, stems, and leaves. The plant-microbe interaction may be advantageous with respect nutrition, development, and stress tolerance of the plant. Mycorrhizal fungi play a vital role in sustaining plant growth and development by supplying nutrients, shielding plants from pathogens, thereby enhancing crop production. Metabolic profiling of both plants and their associated microbes helps researchers to understand expression of their complex biochemical pathways in relation to symbiosis, disease resistance, and stimulating growth. This chapter provides insight into the molecular mechanism linked with this interaction as well as the crucial metabolites affecting microbial colonization, plant immune responses, and the exchange of nutrients specially under mycorrhizal plant-interaction. This interaction helps achieve sustainable agriculture practices, improving plant productivity, soil fertility, and better disease resistance. This chapter discusses the aspects of modulation of metabolomics under abiotic stress, the beneficial microbes, and plant resistance to abiotic stress. This chapter also includes the scopes of metabolomics integration in crop improvement strategies to enhance beneficial plant-microbe interaction and hence crop productivity.