Rice (Oryza sativa L.) consumption is a major route of dietary exposure to arsenic (As). One main reason for the high accumulation of As in rice grain is the high bioavailability of As in porewater of flooded paddy soil. Recently, it has been shown that the application of soil microbial fuel cell (sMFC) can significantly reduce soil porewater As concentration, however, the effect of sMFC on As accumulation in rice is unknown. In this study, a pot experiment was performed to investigate As distribution in rice tissues and the functional microbial communities in soil when the sMFC was installed. The results suggest that the sMFC can simultaneously work as an electricity generator and As mitigator. The total As concentrations in the stems, leaves, husks, and rice grains were significantly decreased by 53.4%, 44.7%, 62.6%, and 67.9%, respectively in the plants with sMFC compared to the control. This decrease in As accumulation in the sMFC treatment may be explained by the decrease in the As reducing arrC gene abundance and soil porewater dissolve organic matter content. The sMFC also significantly increased the relative abundance of the As oxidizing aioA and the As methylation arsM genes which also may have favored the decrease in porewater As. Therefore, the sMFC offers a promising way to mitigate As accumulation in rice tissue and reduce dietary As exposure, while simultaneously producing electricity.