In the face of escalating soil degradation, particularly in regions prone to salt–alkaline stress, sustainable agricultural practices are becoming increasingly critical. Salt–alkaline conditions compromise plant health, reduce crop yields, and hinder agricultural productivity. One promising avenue for mitigating these stressors is through the use of soil microbes that can enhance plants' resilience to abiotic stress. This research investigates the role of microbial consortia in alleviating salt–alkaline stress in fruit crops, with a focus on the integration of plant-growth-promoting rhizobacteria (PGPR) and mycorrhizal fungi to improve nutrient uptake, enhance the soil structure, and promote plants' stress tolerance mechanisms. By leveraging molecular biology techniques, including metabolomics and transcriptomics, we explored the synergistic interactions between plant hosts and microbial communities under saline–alkaline conditions. Our findings highlight the critical role of microbial diversity in modulating plants' stress responses, enhancing their root architecture, and improving osmotic balance within plants. The application of microbial inoculants showed a significant reduction in stress-induced metabolic disruptions while simultaneously increasing the overall plant biomass, yield, and fruit quality in species like citrus and tomato. This research not only demonstrates the potential of microbial-based solutions to improve resilience to environmental stresses but also offers a promising strategy for restoring degraded agricultural lands. These results could contribute to the development of more resilient agricultural systems and support the transition towards sustainable practices that bridge the gap between ecological restoration and food production.