Mexico’s diverse ecosystems host native legumes capable of thriving under contrasting environmental conditions, from the arid coastal dunes of Baja California to the temperate mountains of Michoacán. While beneficial microbes are key to plant health, traditional bioinoculants based on single strains often fail to adapt when applied in the field due to a lack of ecological complexity. Our objective is to move beyond simple isolation and understand how microbial communities assemble and function as a whole to support plant resilience. Focusing on the native species Psorothamnus emoryi and Dalea versicolor, we integrate field physiology, metabolomics, and metagenomics to characterize their root microbiomes and exudates. Using a Synthetic Ecology approach, we will design and assemble multi-species Synthetic Communities (SynComs) that are functionally robust and capable of forming biofilms. These microbial consortia will be tested on Alfalfa (Medicago sativa) to evaluate their ability to enhance crop resilience against biotic and abiotic stressors, such as drought, low nitrogen availability, and pathogens like Fusarium.