Plant–microbe interactions play a fundamental role in regulating plant growth, nutrient acquisition, stress adaptation, and overall ecosystem stability, making them increasingly important in the development of climate-resilient agricultural systems. Beneficial microorganisms, including plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), endophytes, and other rhizospheric microbes, enhance plant productivity through diverse mechanisms such as biological nitrogen fixation, phosphate solubilization, phytohormone production, and pathogen suppression. This review provides a comprehensive overview of the ecological, physiological, and molecular foundations of plant– microbe interactions, emphasizing their role in improving plant tolerance against major abiotic stresses such as drought, salinity, temperature extremes, oxidative stress, heavy metal toxicity, and nutrient deficiency, as well as resistance against biotic stresses. Particular attention is given to stress signaling pathways involving reactive oxygen species, calcium signaling, phytohormonal crosstalk, pattern-triggered immunity, and effector-triggered immunity that mediate adaptive plant responses. The review further examines recent advances in microbiomebased technologies, including multi-omics approaches, systems biology, artificial intelligence, synthetic biology, and phytomicrobiome engineering, which are transforming plant–microbe research from descriptive to predictive and engineering-driven frameworks. Although microbial interventions offer promising alternatives to chemical-intensive agriculture, challenges related to field-level consistency, microbial establishment, biosafety, and largescale adoption remain significant. Integrating mechanistic insights with advanced computational and bio-digital technologies offers substantial potential for designing nextgeneration microbial solutions that enhance crop resilience, improve resource-use efficiency, and support sustainable agriculture under changing climatic conditions.