Root exudates play a crucial role in shaping the rhizosphere microbiome, influencing plant health and resilience against biotic stress. These exudates, composed of sugars, organic acids, amino acids, and secondary metabolites, act as chemical signals that modulate microbial recruitment, fostering beneficial interactions while suppressing pathogens. This study investigates the dynamic role of root exudates in regulating microbial communities and enhancing disease resistance in tomato (Solanum lycopersicum) and citrus (Citrus spp.) under pathogen stress caused by Pseudomonas syringae, P. viridiflava, and Bacillus cereus. Using metabolomics and microbiome sequencing, we analyzed root exudate composition and its influence on rhizosphere microbial diversity. Results indicate that plants under pathogen attack upregulate the secretion of flavonoids, phenolics, and organic acids, thereby significantly enhancing the abundance of beneficial bacteria, including non-pathogenic strains of Pseudomonas and Bacillus spp. while suppressing pathogenic counterparts. Furthermore, transcriptomic analysis reveals the activation of genes associated with exudate biosynthesis and microbial recognition pathways. Inoculation with selected beneficial rhizobacteria further amplified systemic resistance, reducing disease severity through induced systemic resistance (ISR) and competitive exclusion of pathogens. These findings underscore the critical role of root exudates in engineering beneficial microbial consortia, offering potential applications for sustainable crop protection. Harnessing this plant-microbe interaction could lead to the development of microbiome-based biocontrol strategies, reducing reliance on chemical pesticides and improving crop resilience against emerging pathogens. Future research should focus on optimizing root exudate-mediated microbial recruitment to enhance agricultural sustainability.