Beneficial microbial agents, renowned for their cost-effectiveness, high efficiency, and environmental sustainability, play a pivotal role in enhancing plant growth, crop yield, and tolerance to abiotic stresses. This research delves into the impact of the GB03 microbial agent on the fruit quality of ‘Cabernet Sauvignon’ grapes, as well as on soil physicochemical properties and microbial communities under saline stress. The findings revealed that salt-alkali stress significantly elevated soil electrical conductivity, pH, Na⁺ levels, and total salt content, while it markedly reduced soil K⁺, organic matter, ammonium nitrogen, and nitrate nitrogen levels compared to the control. The application of the GB03 microbial agent, however, successfully mitigated these detrimental effects of salt-alkali stress. Furthermore, it augmented the population and abundance of dominant soil bacteria, including Acidobacteriota, Bdellovibrionota, and Gemmatimonadota etc., under saline conditions. Crucially, the microbial agent also inhibited the salt-alkali stress-induced decline in grape fruit’s single cluster weight, 100-grain weight, fruit color intensity, and volatile aroma compounds, as well as the increase in organic acids. Consequently, the GB03 microbial agent emerges as a potent strategy for ameliorating saline-alkali soils and bolstering the salt-alkali stress resilience of horticultural crops like grapes.