Sustainable agriculture systems incorporate important stabilizing mechanisms, such as mulching, for increasing yield and improving soil health. However, the synergistic effects of different long-term mulching practices on soybean yield stability and soil health remain unexplored. In this study, we conducted a 13-year long-term investigation to evaluate the impacts of various mulching methods—no mulching (CK), straw mulching (SM), plastic mulching (PM), and ridged and plastic mulching (RM)—over a 13-year period on soil nutrients, and soybean yield, stability, and sustainability. Our findings revealed that SM, PM, and RM treatments significantly increased the average yields by 28.02 %, 20.49 %, and 51.56 %, respectively. Moreover, SM and RM treatments significantly enhanced yield stability (SM +107.90 %, RM +98.82 %) and sustainability (SM +47.85 %, RM +37.14 %). Additionally, compared to CK, the SM treatment significantly increased the average soil organic carbon (SOC) and total nitrogen (STN) content by 16.78 % and 16.23 %, respectively. Meanwhile, mulching practices also improved soil reactive carbon and nitrogen pools. Compared to CK, plastic mulch reduced microbial biomass carbon (MBC) content (PM −8.85 %, RM −0.73 %) and soil ammonium nitrogen (AN) content (PM −8.19 %, RM −1.20 %), while increasing microbial biomass nitrogen (MBN) content (PM +8.73 %, RM +9.47 %). The SM treatment increased MBC, AN, and MBN contents by 0.24 %, 7.23 %, and 8.94 %, respectively. Additionally, SM and RM treatments significantly increased β-1,4-glucosidase (BG) activity (SM +98.74 %, RM +128.25 %) and decreased and β-1,4- n -acetamido-glucosidase (NAG) + 1-leucine aminopeptidase (LAP) (NAG + LAP) activity (SM −28.74 %, RM −25.33 %) compared to CK. Furthermore, SM, PM, and RM treatments significantly increased the Chao1 index by 35.30 %, 68.08 %, and 52.23 %, respectively, compared to CK. Finally, results of the Mantel test and random forest model indicated that the increases in yield and stability were due to improved soil temperature (ST), active carbon and nitrogen pools, enzyme activity, and diazotrophic bacterial diversity. In summary, our findings suggest that ridged and plastic mulching enhances soil nutrient effectiveness by maintaining soil moisture and regulating diazotrophic bacterial community structure, thereby increasing soybean yields. Conversely, straw mulching continuously supplies nutrients to the soil, enhancing soil quality and diazotrophic bacterial community structure, thus improving yield stability. Over all, our findings provides new insights into global long-term agricultural sustainability.