Chromium (Cr), recognized as a deleterious metal, is ubiquitously present in soil-rice systems, posing a considerable risk to human health through the food chain. However, the controlling factors of Cr transfer from the soil to the paddy system remains largely unknown. This study aimed to examine the transfer patterns of Cr in paddy soil systems during the whole growing periods by comparatively using two series of Cr-contaminated typical agricultural soils. The results showed that the paddy cultivated in lower Cr-contaminated soil exhibited higher bioaccumulation factors (BAFs) due to the greater proportion of bioavailable Cr, in contrast to paddy grown in higher Cr-contaminated soil. Besides, the proportion of residual Cr in the rhizosphere soil notably decreased, and the residual Cr demonstrated a significant negative correlation with the total contents of Fe (p<
0.05) and Mn (p<
0.05). It suggests that the increase in Fe and Mn content promotes the transformation of Cr into bioavailable forms, thereby intensifying the migration of Cr from the soil to the paddy system. Moreover, it was found that Leptothrix that mediate the formation of manganese oxides and Cellulomonas that reduce Fe(III) may be directly or indirectly involved in the activation of Cr in soil. Microbial species such.as Dechloromonas, Candidatus, Rathayibacter and Vogesella, which showed significant correlations with oxidizable and reducible Cr, may play a pivotal role in modulating the bioavailability of Cr in soil by facilitating oxidation and reduction reactions. All these findings contribute to an enhanced comprehension of the pivotal factors governing the transfer of Cr from paddy soils to rice tissues, shedding light on their roles and functions in this process. They have significant implications for initiating appropriate decisions regarding the management of Cr contamination and the implementation of control strategies in paddy systems.