Purpose <p>Bacteria-mediated iron (Fe) cycling in paddy soil modulates arsenic (As) mobility and bioavailability. However, the influence of Fe cycling on the abundance and community diversity of As-related genes that directly affect As species and mobility during flooding and drainage periods is still not fully understood.</p> Methods <p>The measurement of As species, Fe species and fractions, as well as As-cycling microorganisms, aims to uncover the dynamics of As and its related microorganisms in paddy soil amended with ferrihydrite (Fh) under flooding and drainage conditions.</p> Results <p>The results showed that Fh addition reduced As mobility and enhanced As adsorption during flooding and drainage periods. During the flooding stage, Fh marginally impeded the reduction of As(V), whereas Fh facilitated As(III) oxidation during the drainage stage. A positive correlation was observed between the dissolved As(III) concentration and the abundance of the <i>arrA</i> gene, which mediates dissimilatory As(V) reduction. A similar trend was found between the As(V) concentration and the <i>aioA</i> gene, which mediates As(III) oxidation. Moreover, the addition of Fh affected the abundance and community members of <i>arrA</i> and <i>aioA</i> genes, with the dominant <i>aioA</i> operational taxonomic units (OTUs) exhibiting a positive correlation with dissolved Fe(III) concentrations. The redox bacterial communities related to metal transformation exhibited differences in the treatments with Fh and As(V). These suggest a cryptic influence of Fe oxides on microbial As transformation.</p> Conclusion <p>Our findings affirm the critical role of Fe redox transformation in mediating microbial As transformation in paddy soil and provide a theoretically feasible strategy for mitigating As pollution under different watering conditions.</p>