The interaction between plants and beneficial microbes is crucial for enhancing plant productivity, with a specific focus on strengthening plant health and productivity. Metabolomics emerges as a novel approach currently under exploration to confer plant health and fitness, particularly against biotic stress responses. It presents a promising avenue for identifying various metabolites produced to improve stress tolerance and stimulate plant defense mechanisms. However, exploring the metabolomics approach to elucidate microbial contributions to enhancing plant resilience against diseases leaves many questions unanswered. Metabolomics can be utilized to elucidate complex interactions between plants and microbes, emphasizing microbial contributions to enhance plant health. Metabolomics analyses, including gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), high-performance liquid chromatography (HPLC), and nuclear magnetic resonance (NMR), among others, can be employed to unravel complex plant metabolic and signaling pathways. Understanding these metabolites and pathways is key to exploiting the diverse potential of microbes for stress mitigation and improved plant health. Therefore, metabolomics analysis offers the opportunity to detect and identify microbial metabolites while profiling changes in plant metabolomes in response to microbial interactions. This chapter also examines future opportunities and challenges associated with metabolomics in plant-microbe studies, thereby paving the way for the exploration of future prospects in this field.