Soils with greater microbial diversity are generally considered healthier. Cover crops are used to diversify the cropping system, providing various benefits to the agricultural system. After cutting, these crops are sometimes incorporated into the soil and other times left on the surface. This study aimed to evaluate the effects of deposition methods (left on the soil surface or incorporated into the soil) for sunn hemp Crotalaria juncea (CJ) after cutting on soil microbial diversity. A field experiment was conducted with the following treatments in three replications: CJ incorporated (INC), CJ left on the soil surface (SUP), and a control with spontaneous vegetation (CTL). Later, the plots were sown with grain sorghum (MG2220). Soil samples from the 0-10 cm layer were collected 19, 52, and 80 days after CJ cutting and analyzed for microbial diversity. In the first sampling collection, the bacterial diversity in the INC and SUP groups was significantly higher than in the CTL group, likely due to the input of carbon and nitrogen from CJ, stimulating bacterial growth and diversity. However, there was no initial effect on soil fungal diversity. In the second sampling collection, the bacterial diversity in the INC group, the only treatment group that did not receive topdressing with urea (CO(NH₂)₂), was approximately double that of the other treatments, while the fungal diversity remained without significant differences between treatments. Finally, in the third sampling collection, there was no difference between treatments for bacterial or fungal diversity. It was concluded that, for up to 19 days, CJ residues stimulated bacterial diversity. Urea nitrogen topdressing negatively influenced bacterial diversity. At 80 days after CJ cutting, the bacterial diversity decreased compared to the first sampling round, and the fungal diversity was not significantly affected by the treatments evaluated.