To investigate the effects of different types of microbial agents applied during the jointing stage of wheat in a wheat-maize rotation system on soil properties, a field experiment was conducted from 2022 to 2024. Four treatments were set up: a water control (CK), application of auxin-producing microbial agent (T1), application of microbial agent (T2), and application of biocontrol microbial agent (T3). The impacts of these agents on soil chemical properties, bacterial community structure, and wheat yield were examined. The results showed that in the 0-20 cm soil layer, the application of various microbial agents significantly improved soil chemical properties compared to CK. The T2 treatment had the most significant effect on increasing soil alkaline nitrogen and available phosphorus content, with increases of 22.60%-29.61% and 21.63%-37.51%, respectively, and a significant decrease in pH value, while there was no significant difference in available potassium content among all treatments. In the 20-40 cm soil layer, the available phosphorus content in the T2 treatment was significantly higher than that in CK by 22.05%, and there were no significant differences in pH value, organic matter, alkaline nitrogen, and available potassium content among all treatments. Compared to CK, the application of all microbial agents was conducive to increasing the α-diversity index of rhizosphere soil bacteria, with an increase of 2.59%-3.29%. The application of microbial agents significantly affected the relative abundance of dominant bacterial phyla in the soil. Ninety days after application, compared to CK, the relative abundance of Proteobacteria in the T1, T2, and T3 treatments increased significantly by 2.70%, 5.42%, and 3.71%, respectively, while the relative abundance of Gemmatimonadetes in the T2 treatment decreased significantly by 4.75%. The relative abundance of bacteria with biocontrol and growth-promoting functions in the rhizosphere soil of all microbial agent treatments was higher than that in the CK treatment, while the relative abundance of the pathogenic Nocardioides, which has disease-inducing effects, was significantly reduced at both 15 and 90 days. Compared to CK, the wheat yield in the microbial agent treatments increased significantly by 8.28%-20.43% in 2022-2023 and by 5.70%-16.23% in 2023-2024, with the T2 treatment showing the most significant effect. In conclusion, the application of microbial agents during the jointing stage of wheat effectively activated soil nutrients, enhanced bacterial diversity and the abundance of biocontrol/promotive function bacteria, and increased wheat yield, with the application of Pseudomonas fluorescens PM12 being the most effective.