Salvia miltiorrhiza is a widely used medicinal plant, and post-harvest processing methods such as sweating may influence its metabolite composition and microbial interactions. However, the metabolic and microbial changes induced by sweating remain poorly understood. This study aimed to investigate how sweating affects the metabolite profile of S. miltiorrhiza and its associated bacterial communities, with a focus on identifying key metabolic shifts and microbial dynamics. Widely targeted metabolomics was employed to compare the composition and relative content of metabolites between control (non-sweated) and sweated S. miltiorrhiza plants. Additionally, high-throughput sequencing was used to analyze variations in bacterial communities at different sweating stages. A total of 435 differentially present metabolites were identified, categorized into 11 classes, with quinones, phenolic acids, and lipids being the most prominent. Sweating significantly increased microbial diversity and richness, and we established a correlation between the accumulation of quinones and phenolic acids and shifts in bacterial community structure. Notably, sweating enhanced the levels of key metabolites, which in turn promoted the relative abundance of potentially beneficial microorganisms. Furthermore, distinct bacterial populations at different sweating stages contributed to the unique quality traits of S. miltiorrhiza. The findings demonstrate that sweating not only alters the metabolite profile of S. miltiorrhiza but also shapes its associated bacterial communities, leading to improved accumulation of bioactive compounds.