To overcome this challenge, the incorporation of comprehensive environmental data into metabolomics studies is of utmost importance. By capturing the complex interplay between biotic and abiotic factors, researchers can gain a deeper understanding of the context-dependent metabolic responses that govern the dynamic relationships between plants and their microbial partners. Addressing the confounding influence of abiotic factors on metabolomics data interpretation will require the development of advanced experimental designs, advanced analytical techniques, and sophisticated computational tools . Integrating environmental monitoring, high-resolution metabolic profiling, and data-driven modeling will be crucial in unraveling the metabolic signatures that are intrinsically linked to the success or failure of plant-microbe interactions across diverse environmental settings. Overcoming this challenge will pave the way for the identification of robust metabolic markers and the design of targeted strategies to enhance the resilience and productivity of plant-microbe systems in the face of dynamic environmental pressures.