<p>Rice ratooning has received increased attention in recent years since it can reduce labor, seed, and energy inputs. However, rice ratooning may result in yield loss and thus requires the addition of fertilizers. In addition, some recent research has indicated that rice ratooning can significantly reduce the concentration of grain arsenic (As). Therefore, pot experiments were conducted in the present study to delineate the effects of different fertilizers on grain As accumulation in ratoon rice from three rice genotypes commonly cultivated in Taiwan. The interaction between iron (Fe) and As in rhizosphere soil and the root surface was also determined. The results showed that fertilizer treatment had profound effects on As accumulation in Fe plaque. In addition, there was a remarkable difference in the indexes of As sequestration by Fe oxides in root plaque (<i>IAS</i>) among the three cultivars. Significant correlations were found between As in brown rice and <i>IAS</i> across three genotypes and five fertilizers treatments, with the <i>r</i>² value ranging from 0.3933 to 0.8708. This result implies the feasibility of reducing As concentrations in grains by managing <i>IAS</i> in an Fe plaque environment in the rice ratooning system. Moreover, rice husk treatment showed different effects on As accumulation in the different rice genotypes, indicating that different fertilizer application strategies should be adopted for different genotypes to reduce As accumulation in ratoon rice. Lastly, according to the assessment results, the selection of TCS17 along with the application of 0.5–1% rice husk could effectively reduce the health risks associated with consuming ratoon rice. This study clarified the effects of fertilizers on As accumulation in ratoon rice, and future research is encouraged to characterize the effects of various factors on the accumulation and translocation of As in a rice ratoon system.</p>