Background and Aims <p>Microbial communities in mangrove sediments are crucial to the biogeochemical cycles in mangrove ecosystems. The impact of sedimentary environment on the characteristics of microbial communities under the mangrove plantations of the Qingjiang Estuary (Zhejiang Province, China) has not been widely researched at in-situ macroscopic level.</p> Methods <p>This study investigated the structures and dynamic mechanisms of microbial communities by analyzing 32 sediment samples across different vegetation zones in June 2023. Principal coordinates analysis, principal component analysis, Spearman correlation, and redundancy analysis were applied to examine the dynamic interplay between environmental factors and microbial communities.</p> Results <p>Results showed that significant differences in the sedimentary environment and microbial communities were detected within the vegetation zones. Utilizing the alpha diversity indices of Chao1 and Shannon, it was observed that the highest species richness and diversity were detected in the <i>Spartina alterniflora</i> zone. <i>Proteobacteria</i> (accounting for 40.0%) and <i>Desulfobacterota</i> (12.9%) were the dominant species at the phylum level that accounted for the significant variations observed in the microbial communities. <i>Woeseia</i> (10.7%) exhibited the highest relative abundance at the genus level in sediments, followed by <i>Sulfurovum</i> (4.6%). Nitrogen and redox potential were the most important factors affecting the microbial community structures.</p> Conclusions <p>Mangrove planting significantly altered the microbial community structure by changing sediment nitrogen levels and redox potential. Compared to the <i>Spartina alterniflora</i> zone, the dominant taxa composition and functional metabolic pathways in the mangrove-planted zone showed distinct differentiation, with dynamic changes in <i>Proteobacteria</i> and <i>Desulfobacterota</i> closely associated with carbon and nitrogen cycling processes.</p>